3OTO | pdb_00003oto

Crystal Structure of the 30S ribosomal subunit from a KsgA mutant of Thermus thermophilus (HB8)

PDB DOI: https://doi.org/10.2210/pdb3OTO/pdb
NAKB: 3OTO

Classification: RIBOSOME
Organism(s): Thermus thermophilus HB8
Mutation(s): No

Deposited: 2010-09-13 Released: 2010-09-29
Deposition Author(s): Demirci, H., Murphy IV, F., Belardinelli, R., Kelley, A.C., Ramakrishnan, V., Gregory, S.T., Dahlberg, A.E., Jogl, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.69 Å
R-Value Free:
0.231 (Depositor), 0.228 (DCC)
R-Value Work:
0.173 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function.

Demirci, H., Murphy, F., Belardinelli, R., Kelley, A.C., Ramakrishnan, V., Gregory, S.T., Dahlberg, A.E., Jogl, G.

(2010) RNA 16: 2319-2324

PubMed: 20962038 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1261/rna.2357210
Primary Citation Related Structures:
3OTO

PubMed Abstract:
All organisms incorporate post-transcriptional modifications into ribosomal RNA, influencing ribosome assembly and function in ways that are poorly understood. The most highly conserved modification is the dimethylation of two adenosines near the 3' end of the small subunit rRNA. Lack of these methylations due to deficiency in the KsgA methyltransferase stimulates translational errors during both the initiation and elongation phases of protein synthesis and confers resistance to the antibiotic kasugamycin. Here, we present the X-ray crystal structure of the Thermus thermophilus 30S ribosomal subunit lacking these dimethylations. Our data indicate that the KsgA-directed methylations facilitate structural rearrangements in order to establish a functionally optimum subunit conformation during the final stages of ribosome assembly.

Organizational Affiliation

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

Macromolecule Content

Total Structure Weight: 787.73 kDa
Atom Count: 51,775
Modeled Residue Count: 3,900
Deposited Residue Count: 4,063
Unique protein chains: 20
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S2	B	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371 Go to UniProtKB: P80371
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80371
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	C	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372 Go to UniProtKB: P80372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80372
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	D	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373 Go to UniProtKB: P80373
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80373
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	E	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5 Go to UniProtKB: Q5SHQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	F	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8 Go to UniProtKB: Q5SLP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLP8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	G	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291 Go to UniProtKB: P17291
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17291
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	H	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9 Go to UniProtKB: P0DOY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	I	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374 Go to UniProtKB: P80374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80374
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	J	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7 Go to UniProtKB: Q5SHN7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	K	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376 Go to UniProtKB: P80376
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80376
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	L	135	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3 Go to UniProtKB: Q5SHN3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHN3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	M	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377 Go to UniProtKB: P80377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80377
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14	N	61	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6 Go to UniProtKB: P0DOY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	O	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76 Go to UniProtKB: Q5SJ76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJ76
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	P	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3 Go to UniProtKB: Q5SJH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SJH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	Q	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7 Go to UniProtKB: P0DOY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	R	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0 Go to UniProtKB: Q5SLQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SLQ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	S	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2 Go to UniProtKB: Q5SHP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHP2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	T	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380 Go to UniProtKB: P80380
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80380
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN THX	U	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3 Go to UniProtKB: Q5SIH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIH3
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
16S rRNA	A	1,522	Thermus thermophilus HB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain YE [auth D] SDF format, chain CF [auth N] MOL2 format, chain YE [auth D] MOL2 format, chain CF [auth N] mmCIF format, chain YE [auth D] mmCIF format, chain CF [auth N]	CF [auth N], YE [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CF [auth N] Focus chain YE [auth D] Interactions & Density Focus chain CF [auth N] Focus chain YE [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain ZD [auth A] SDF format, chain YD [auth A] SDF format, chain XD [auth A] SDF format, chain WE [auth A] SDF format, chain WD [auth A] SDF format, chain VE [auth A] SDF format, chain VD [auth A] SDF format, chain UE [auth A] SDF format, chain UD [auth A] SDF format, chain TE [auth A] SDF format, chain TD [auth A] SDF format, chain SE [auth A] SDF format, chain SD [auth A] SDF format, chain RE [auth A] SDF format, chain RD [auth A] SDF format, chain QE [auth A] SDF format, chain QD [auth A] SDF format, chain PE [auth A] SDF format, chain PD [auth A] SDF format, chain OE [auth A] SDF format, chain OD [auth A] SDF format, chain NE [auth A] SDF format, chain ND [auth A] SDF format, chain ME [auth A] SDF format, chain MD [auth A] SDF format, chain LE [auth A] SDF format, chain LD [auth A] SDF format, chain KE [auth A] SDF format, chain KD [auth A] SDF format, chain JE [auth A] SDF format, chain JD [auth A] SDF format, chain IE [auth A] SDF format, chain ID [auth A] SDF format, chain HE [auth A] SDF format, chain GE [auth A] SDF format, chain FE [auth A] SDF format, chain EE [auth A] SDF format, chain DE [auth A] SDF format, chain CE [auth A] SDF format, chain BE [auth A] SDF format, chain AF [auth E] SDF format, chain AE [auth A] MOL2 format, chain ZD [auth A] MOL2 format, chain YD [auth A] MOL2 format, chain XD [auth A] MOL2 format, chain WE [auth A] MOL2 format, chain WD [auth A] MOL2 format, chain VE [auth A] MOL2 format, chain VD [auth A] MOL2 format, chain UE [auth A] MOL2 format, chain UD [auth A] MOL2 format, chain TE [auth A] MOL2 format, chain TD [auth A] MOL2 format, chain SE [auth A] MOL2 format, chain SD [auth A] MOL2 format, chain RE [auth A] MOL2 format, chain RD [auth A] MOL2 format, chain QE [auth A] MOL2 format, chain QD [auth A] MOL2 format, chain PE [auth A] MOL2 format, chain PD [auth A] MOL2 format, chain OE [auth A] MOL2 format, chain OD [auth A] MOL2 format, chain NE [auth A] MOL2 format, chain ND [auth A] MOL2 format, chain ME [auth A] MOL2 format, chain MD [auth A] MOL2 format, chain LE [auth A] MOL2 format, chain LD [auth A] MOL2 format, chain KE [auth A] MOL2 format, chain KD [auth A] MOL2 format, chain JE [auth A] MOL2 format, chain JD [auth A] MOL2 format, chain IE [auth A] MOL2 format, chain ID [auth A] MOL2 format, chain HE [auth A] MOL2 format, chain GE [auth A] MOL2 format, chain FE [auth A] MOL2 format, chain EE [auth A] MOL2 format, chain DE [auth A] MOL2 format, chain CE [auth A] MOL2 format, chain BE [auth A] MOL2 format, chain AF [auth E] MOL2 format, chain AE [auth A] mmCIF format, chain ZD [auth A] mmCIF format, chain YD [auth A] mmCIF format, chain XD [auth A] mmCIF format, chain WE [auth A] mmCIF format, chain WD [auth A] mmCIF format, chain VE [auth A] mmCIF format, chain VD [auth A] mmCIF format, chain UE [auth A] mmCIF format, chain UD [auth A] mmCIF format, chain TE [auth A] mmCIF format, chain TD [auth A] mmCIF format, chain SE [auth A] mmCIF format, chain SD [auth A] mmCIF format, chain RE [auth A] mmCIF format, chain RD [auth A] mmCIF format, chain QE [auth A] mmCIF format, chain QD [auth A] mmCIF format, chain PE [auth A] mmCIF format, chain PD [auth A] mmCIF format, chain OE [auth A] mmCIF format, chain OD [auth A] mmCIF format, chain NE [auth A] mmCIF format, chain ND [auth A] mmCIF format, chain ME [auth A] mmCIF format, chain MD [auth A] mmCIF format, chain LE [auth A] mmCIF format, chain LD [auth A] mmCIF format, chain KE [auth A] mmCIF format, chain KD [auth A] mmCIF format, chain JE [auth A] mmCIF format, chain JD [auth A] mmCIF format, chain IE [auth A] mmCIF format, chain ID [auth A] mmCIF format, chain HE [auth A] mmCIF format, chain GE [auth A] mmCIF format, chain FE [auth A] mmCIF format, chain EE [auth A] mmCIF format, chain DE [auth A] mmCIF format, chain CE [auth A] mmCIF format, chain BE [auth A] mmCIF format, chain AF [auth E] mmCIF format, chain AE [auth A]	AE [auth A] AF [auth E] BE [auth A] CE [auth A] DE [auth A] AE [auth A], AF [auth E], BE [auth A], CE [auth A], DE [auth A], EE [auth A], FE [auth A], GE [auth A], HE [auth A], ID [auth A], IE [auth A], JD [auth A], JE [auth A], KD [auth A], KE [auth A], LD [auth A], LE [auth A], MD [auth A], ME [auth A], ND [auth A], NE [auth A], OD [auth A], OE [auth A], PD [auth A], PE [auth A], QD [auth A], QE [auth A], RD [auth A], RE [auth A], SD [auth A], SE [auth A], TD [auth A], TE [auth A], UD [auth A], UE [auth A], VD [auth A], VE [auth A], WD [auth A], WE [auth A], XD [auth A], YD [auth A], ZD [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AE [auth A] Focus chain AF [auth E] Focus chain BE [auth A] Focus chain CE [auth A] Focus chain DE [auth A] Focus chain EE [auth A] Focus chain FE [auth A] Focus chain GE [auth A] Focus chain HE [auth A] Focus chain ID [auth A] Focus chain IE [auth A] Focus chain JD [auth A] Focus chain JE [auth A] Focus chain KD [auth A] Focus chain KE [auth A] Focus chain LD [auth A] Focus chain LE [auth A] Focus chain MD [auth A] Focus chain ME [auth A] Focus chain ND [auth A] Focus chain NE [auth A] Focus chain OD [auth A] Focus chain OE [auth A] Focus chain PD [auth A] Focus chain PE [auth A] Focus chain QD [auth A] Focus chain QE [auth A] Focus chain RD [auth A] Focus chain RE [auth A] Focus chain SD [auth A] Focus chain SE [auth A] Focus chain TD [auth A] Focus chain TE [auth A] Focus chain UD [auth A] Focus chain UE [auth A] Focus chain VD [auth A] Focus chain VE [auth A] Focus chain WD [auth A] Focus chain WE [auth A] Focus chain XD [auth A] Focus chain YD [auth A] Focus chain ZD [auth A] Interactions & Density Focus chain AE [auth A] Focus chain AF [auth E] Focus chain BE [auth A] Focus chain CE [auth A] Focus chain DE [auth A] Focus chain EE [auth A] Focus chain FE [auth A] Focus chain GE [auth A] Focus chain HE [auth A] Focus chain ID [auth A] Focus chain IE [auth A] Focus chain JD [auth A] Focus chain JE [auth A] Focus chain KD [auth A] Focus chain KE [auth A] Focus chain LD [auth A] Focus chain LE [auth A] Focus chain MD [auth A] Focus chain ME [auth A] Focus chain ND [auth A] Focus chain NE [auth A] Focus chain OD [auth A] Focus chain OE [auth A] Focus chain PD [auth A] Focus chain PE [auth A] Focus chain QD [auth A] Focus chain QE [auth A] Focus chain RD [auth A] Focus chain RE [auth A] Focus chain SD [auth A] Focus chain SE [auth A] Focus chain TD [auth A] Focus chain TE [auth A] Focus chain UD [auth A] Focus chain UE [auth A] Focus chain VD [auth A] Focus chain VE [auth A] Focus chain WD [auth A] Focus chain WE [auth A] Focus chain XD [auth A] Focus chain YD [auth A] Focus chain ZD [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZE [auth D] SDF format, chain ZC [auth A] SDF format, chain ZB [auth A] SDF format, chain ZA [auth A] SDF format, chain Z [auth A] SDF format, chain YC [auth A] SDF format, chain YB [auth A] SDF format, chain YA [auth A] SDF format, chain Y [auth A] SDF format, chain XE [auth B] SDF format, chain XC [auth A] SDF format, chain XB [auth A] SDF format, chain XA [auth A] SDF format, chain X [auth A] SDF format, chain WC [auth A] SDF format, chain WB [auth A] SDF format, chain WA [auth A] SDF format, chain W [auth A] SDF format, chain VC [auth A] SDF format, chain VB [auth A] SDF format, chain VA [auth A] SDF format, chain V [auth A] SDF format, chain UC [auth A] SDF format, chain UB [auth A] SDF format, chain UA [auth A] SDF format, chain TC [auth A] SDF format, chain TB [auth A] SDF format, chain TA [auth A] SDF format, chain SC [auth A] SDF format, chain SB [auth A] SDF format, chain SA [auth A] SDF format, chain RC [auth A] SDF format, chain RB [auth A] SDF format, chain RA [auth A] SDF format, chain QC [auth A] SDF format, chain QB [auth A] SDF format, chain QA [auth A] SDF format, chain PC [auth A] SDF format, chain PB [auth A] SDF format, chain PA [auth A] SDF format, chain OC [auth A] SDF format, chain OB [auth A] SDF format, chain OA [auth A] SDF format, chain NC [auth A] SDF format, chain NB [auth A] SDF format, chain NA [auth A] SDF format, chain MC [auth A] SDF format, chain MB [auth A] SDF format, chain MA [auth A] SDF format, chain LC [auth A] SDF format, chain LB [auth A] SDF format, chain LA [auth A] SDF format, chain KC [auth A] SDF format, chain KB [auth A] SDF format, chain KA [auth A] SDF format, chain JC [auth A] SDF format, chain JB [auth A] SDF format, chain JA [auth A] SDF format, chain IC [auth A] SDF format, chain IB [auth A] SDF format, chain IA [auth A] SDF format, chain HD [auth A] SDF format, chain HC [auth A] SDF format, chain HB [auth A] SDF format, chain HA [auth A] SDF format, chain GD [auth A] SDF format, chain GC [auth A] SDF format, chain GB [auth A] SDF format, chain GA [auth A] SDF format, chain FD [auth A] SDF format, chain FC [auth A] SDF format, chain FB [auth A] SDF format, chain FA [auth A] SDF format, chain ED [auth A] SDF format, chain EC [auth A] SDF format, chain EB [auth A] SDF format, chain EA [auth A] SDF format, chain DD [auth A] SDF format, chain DC [auth A] SDF format, chain DB [auth A] SDF format, chain DA [auth A] SDF format, chain CD [auth A] SDF format, chain CC [auth A] SDF format, chain CB [auth A] SDF format, chain CA [auth A] SDF format, chain BF [auth M] SDF format, chain BD [auth A] SDF format, chain BC [auth A] SDF format, chain BB [auth A] SDF format, chain BA [auth A] SDF format, chain AD [auth A] SDF format, chain AC [auth A] SDF format, chain AB [auth A] SDF format, chain AA [auth A] MOL2 format, chain ZE [auth D] MOL2 format, chain ZC [auth A] MOL2 format, chain ZB [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain YC [auth A] MOL2 format, chain YB [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain XE [auth B] MOL2 format, chain XC [auth A] MOL2 format, chain XB [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain X [auth A] MOL2 format, chain WC [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain VC [auth A] MOL2 format, chain VB [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain UC [auth A] MOL2 format, chain UB [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain TC [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain SC [auth A] MOL2 format, chain SB [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain RC [auth A] MOL2 format, chain RB [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain QC [auth A] MOL2 format, chain QB [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain PC [auth A] MOL2 format, chain PB [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain OC [auth A] MOL2 format, chain OB [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain NC [auth A] MOL2 format, chain NB [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MC [auth A] MOL2 format, chain MB [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LC [auth A] MOL2 format, chain LB [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KC [auth A] MOL2 format, chain KB [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JC [auth A] MOL2 format, chain JB [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IC [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HD [auth A] MOL2 format, chain HC [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain GD [auth A] MOL2 format, chain GC [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FD [auth A] MOL2 format, chain FC [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain ED [auth A] MOL2 format, chain EC [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DD [auth A] MOL2 format, chain DC [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CD [auth A] MOL2 format, chain CC [auth A] MOL2 format, chain CB [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BF [auth M] MOL2 format, chain BD [auth A] MOL2 format, chain BC [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AD [auth A] MOL2 format, chain AC [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain ZE [auth D] mmCIF format, chain ZC [auth A] mmCIF format, chain ZB [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain YC [auth A] mmCIF format, chain YB [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain XE [auth B] mmCIF format, chain XC [auth A] mmCIF format, chain XB [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain X [auth A] mmCIF format, chain WC [auth A] mmCIF format, chain WB [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain VC [auth A] mmCIF format, chain VB [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain V [auth A] mmCIF format, chain UC [auth A] mmCIF format, chain UB [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain TC [auth A] mmCIF format, chain TB [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain SC [auth A] mmCIF format, chain SB [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain RC [auth A] mmCIF format, chain RB [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain QC [auth A] mmCIF format, chain QB [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain PC [auth A] mmCIF format, chain PB [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain OC [auth A] mmCIF format, chain OB [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain NC [auth A] mmCIF format, chain NB [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MC [auth A] mmCIF format, chain MB [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LC [auth A] mmCIF format, chain LB [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KC [auth A] mmCIF format, chain KB [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JC [auth A] mmCIF format, chain JB [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IC [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HD [auth A] mmCIF format, chain HC [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain GD [auth A] mmCIF format, chain GC [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FD [auth A] mmCIF format, chain FC [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain ED [auth A] mmCIF format, chain EC [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DD [auth A] mmCIF format, chain DC [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CD [auth A] mmCIF format, chain CC [auth A] mmCIF format, chain CB [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BF [auth M] mmCIF format, chain BD [auth A] mmCIF format, chain BC [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AD [auth A] mmCIF format, chain AC [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth A] AC [auth A] AD [auth A] BA [auth A] AA [auth A], AB [auth A], AC [auth A], AD [auth A], BA [auth A], BB [auth A], BC [auth A], BD [auth A], BF [auth M], CA [auth A], CB [auth A], CC [auth A], CD [auth A], DA [auth A], DB [auth A], DC [auth A], DD [auth A], EA [auth A], EB [auth A], EC [auth A], ED [auth A], FA [auth A], FB [auth A], FC [auth A], FD [auth A], GA [auth A], GB [auth A], GC [auth A], GD [auth A], HA [auth A], HB [auth A], HC [auth A], HD [auth A], IA [auth A], IB [auth A], IC [auth A], JA [auth A], JB [auth A], JC [auth A], KA [auth A], KB [auth A], KC [auth A], LA [auth A], LB [auth A], LC [auth A], MA [auth A], MB [auth A], MC [auth A], NA [auth A], NB [auth A], NC [auth A], OA [auth A], OB [auth A], OC [auth A], PA [auth A], PB [auth A], PC [auth A], QA [auth A], QB [auth A], QC [auth A], RA [auth A], RB [auth A], RC [auth A], SA [auth A], SB [auth A], SC [auth A], TA [auth A], TB [auth A], TC [auth A], UA [auth A], UB [auth A], UC [auth A], V [auth A], VA [auth A], VB [auth A], VC [auth A], W [auth A], WA [auth A], WB [auth A], WC [auth A], X [auth A], XA [auth A], XB [auth A], XC [auth A], XE [auth B], Y [auth A], YA [auth A], YB [auth A], YC [auth A], Z [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZE [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain BF [auth M] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XE [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZE [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth A] Focus chain AC [auth A] Focus chain AD [auth A] Focus chain BA [auth A] Focus chain BB [auth A] Focus chain BC [auth A] Focus chain BD [auth A] Focus chain BF [auth M] Focus chain CA [auth A] Focus chain CB [auth A] Focus chain CC [auth A] Focus chain CD [auth A] Focus chain DA [auth A] Focus chain DB [auth A] Focus chain DC [auth A] Focus chain DD [auth A] Focus chain EA [auth A] Focus chain EB [auth A] Focus chain EC [auth A] Focus chain ED [auth A] Focus chain FA [auth A] Focus chain FB [auth A] Focus chain FC [auth A] Focus chain FD [auth A] Focus chain GA [auth A] Focus chain GB [auth A] Focus chain GC [auth A] Focus chain GD [auth A] Focus chain HA [auth A] Focus chain HB [auth A] Focus chain HC [auth A] Focus chain HD [auth A] Focus chain IA [auth A] Focus chain IB [auth A] Focus chain IC [auth A] Focus chain JA [auth A] Focus chain JB [auth A] Focus chain JC [auth A] Focus chain KA [auth A] Focus chain KB [auth A] Focus chain KC [auth A] Focus chain LA [auth A] Focus chain LB [auth A] Focus chain LC [auth A] Focus chain MA [auth A] Focus chain MB [auth A] Focus chain MC [auth A] Focus chain NA [auth A] Focus chain NB [auth A] Focus chain NC [auth A] Focus chain OA [auth A] Focus chain OB [auth A] Focus chain OC [auth A] Focus chain PA [auth A] Focus chain PB [auth A] Focus chain PC [auth A] Focus chain QA [auth A] Focus chain QB [auth A] Focus chain QC [auth A] Focus chain RA [auth A] Focus chain RB [auth A] Focus chain RC [auth A] Focus chain SA [auth A] Focus chain SB [auth A] Focus chain SC [auth A] Focus chain TA [auth A] Focus chain TB [auth A] Focus chain TC [auth A] Focus chain UA [auth A] Focus chain UB [auth A] Focus chain UC [auth A] Focus chain V [auth A] Focus chain VA [auth A] Focus chain VB [auth A] Focus chain VC [auth A] Focus chain W [auth A] Focus chain WA [auth A] Focus chain WB [auth A] Focus chain WC [auth A] Focus chain X [auth A] Focus chain XA [auth A] Focus chain XB [auth A] Focus chain XC [auth A] Focus chain XE [auth B] Focus chain Y [auth A] Focus chain YA [auth A] Focus chain YB [auth A] Focus chain YC [auth A] Focus chain Z [auth A] Focus chain ZA [auth A] Focus chain ZB [auth A] Focus chain ZC [auth A] Focus chain ZE [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.69 Å
R-Value Free: 0.231 (Depositor), 0.228 (DCC)
R-Value Work: 0.173 (Depositor), 0.175 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 402.089	α = 90
b = 402.089	β = 90
c = 173.254	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3OTO | pdb_00003oto

Crystal Structure of the 30S ribosomal subunit from a KsgA mutant of Thermus thermophilus (HB8)

Literature

Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function.

Biological Assembly 1

Macromolecules

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations

Entity ID: 20

UniProt