4LFC
Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
- PDB DOI: https://doi.org/10.2210/pdb4LFC/pdb
- NAKB: 4LFC
- Classification: RIBOSOME
- Organism(s): Thermus thermophilus HB8
- Mutation(s): No
- Deposited: 2013-06-26 Released: 2014-07-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.60 Å
- R-Value Free: 0.209
- R-Value Work: 0.163
- R-Value Observed: 0.165
This is version 1.0 of the entry. See complete history.
Literature
Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.
To be published.
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S2 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80371 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S3 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80372 | ||||
Sequence AnnotationsExpand | |||||
|
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Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S4 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80373 | ||||
Sequence AnnotationsExpand | |||||
|
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Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S5 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SHQ5 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S6 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SLP8 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 7 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S7 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P17291 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 8 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S8 | 138 | Thermus thermophilus HB8 | Mutation(s): 0 | ||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 9 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S9 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80374 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 10 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S10 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SHN7 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 11 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S11 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80376 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 12 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S12 | 135 | Thermus thermophilus HB8 | Mutation(s): 0 | ||
UniProt | |||||
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16)) Explore F6DEQ7 Go to UniProtKB: F6DEQ7 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | F6DEQ7 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 13 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S13 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80377 | ||||
Sequence AnnotationsExpand | |||||
|
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Entity ID: 14 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S14 | 61 | Thermus thermophilus HB8 | Mutation(s): 0 | ||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 15 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S15 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SJ76 | ||||
Sequence AnnotationsExpand | |||||
|
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Entity ID: 16 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S16 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SJH3 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 17 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S17 | 105 | Thermus thermophilus HB8 | Mutation(s): 0 | ||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 18 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S18 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SLQ0 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 19 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S19 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SHP2 | ||||
Sequence AnnotationsExpand | |||||
|
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(by identity cutoff) | 3D Structure
Entity ID: 20 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein S20 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P80380 | ||||
Sequence AnnotationsExpand | |||||
|
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Entity ID: 21 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
ribosomal protein THX | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q5SIH3 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TOY Query on TOY | CF [auth A] | TOBRAMYCIN C18 H37 N5 O9 NLVFBUXFDBBNBW-PBSUHMDJSA-N | |||
ZN Query on ZN | EF [auth D], MF [auth N] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
K Query on K | AE [auth A] BE [auth A] CE [auth A] DE [auth A] EE [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
MG Query on MG | AA [auth A] AB [auth A] AC [auth A] AD [auth A] AF [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
0TD Query on 0TD | L | L-PEPTIDE LINKING | C5 H9 N O4 S | ASP |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.60 Å
- R-Value Free: 0.209
- R-Value Work: 0.163
- R-Value Observed: 0.165
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 401.831 | α = 90 |
b = 401.831 | β = 90 |
c = 175.888 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2014-07-02 Deposition Author(s): Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.
Revision History (Full details and data files)
- Version 1.0: 2014-07-02
Type: Initial release