6CAP

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin

• PDB DOI: https://doi.org/10.2210/pdb6CAP/pdb
• NAKB: 6CAP

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


• Deposited: 2018-01-31 Released: 2018-07-25 
• Deposition Author(s): DeMirci, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.230 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Literature

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin

DeMirci, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 779.1 kDa 
• Atom Count: 52,675 
• Modelled Residue Count: 3,910 
• Deposited Residue Count: 3,920 
• Unique protein chains: 20
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B	234	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C	206	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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D	208	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 ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN S5	E	150	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 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 ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G	155	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 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 ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I	127	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 ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J	98	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 ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K	116	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 ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L	124	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 ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M	118	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 ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	N	60	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 ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O	87	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 ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P	83	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 ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q	99	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 ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R	70	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 ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S	80	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 ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T	99	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 ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	U	24	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 ID: 1
Molecule	Chains	Length	Organism	Image
16S Ribosomal RNA rRNA	A	1,522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')	V [auth Y]	6	Thermus thermophilus HB8

Entity ID: 23
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')	W	15	Thermus thermophilus HB8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIS	GH [auth A]	(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside C19 H37 N5 O7 URWAJWIAIPFPJE-YFMIWBNJSA-N
ZN	IJ [auth N], OI [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AA [auth A], AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth A], AH [auth A], AI [auth A], AJ [auth L], BA [auth A], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth A], BH [auth A], BI [auth A], BJ [auth L], CA [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth A], CH [auth A], CI [auth A], CJ [auth L], DA [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth A], DH [auth A], DI [auth A], DJ [auth M], EA [auth A], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth A], EH [auth A], EI [auth A], EJ [auth M], FA [auth A], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], FG [auth A], FH [auth A], FI [auth A], FJ [auth M], GA [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GG [auth A], GI [auth B], GJ [auth M], HA [auth A], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth A], HH [auth A], HI [auth B], HJ [auth M], IA [auth A], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], IG [auth A], IH [auth A], II [auth B], JA [auth A], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth A], JH [auth A], JI [auth C], JJ [auth P], KA [auth A], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth A], KH [auth A], KI [auth C], KJ [auth P], LA [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth A], LH [auth A], LI [auth C], LJ [auth P], MA [auth A], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], MG [auth A], MH [auth A], MI [auth C], MJ [auth Q], NA [auth A], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], NG [auth A], NH [auth A], NI [auth C], NJ [auth Q], OA [auth A], OB [auth A], OC [auth A], OD [auth A], OE [auth A], OF [auth A], OG [auth A], OH [auth A], OJ [auth Q], PA [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth A], PI [auth D], PJ [auth S], QA [auth A], QB [auth A], QC [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth A], QH [auth A], QI [auth D], QJ [auth T], RA [auth A], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RF [auth A], RG [auth A], RH [auth A], RI [auth D], RJ [auth W], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SF [auth A], SG [auth A], SH [auth A], SI [auth E], TA [auth A], TB [auth A], TC [auth A], TD [auth A], TE [auth A], TF [auth A], TG [auth A], TH [auth A], TI [auth F], UA [auth A], UB [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth A], UG [auth A], UH [auth A], UI [auth H], VA [auth A], VB [auth A], VC [auth A], VD [auth A], VE [auth A], VF [auth A], VG [auth A], VH [auth A], VI [auth H], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth A], WG [auth A], WH [auth A], WI [auth K], X [auth A], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XF [auth A], XG [auth A], XH [auth A], XI [auth K], Y [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], YH [auth A], YI [auth K], Z [auth A], ZA [auth A], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZF [auth A], ZG [auth A], ZH [auth A], ZI [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0TD	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.230 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 400.97	α = 90
b = 400.97	β = 90
c = 175.05	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): DeMirci, H.

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Data collection, Derived calculations