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Download EndnoteA structural basis for streptomycin resistance
Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.To be published.
4DV0
Crystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, U20G
- DOI: 10.2210/pdb4DV0/pdb
- NDB: NA1617
- Classification: RIBOSOME
- Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus aquaticus, Thermus thermophilus HB8
- Mutation(s): 1
- Deposited: 2012-02-22 Released: 2013-02-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.853 Å
- R-Value Free: 0.206
- R-Value Work: 0.147
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S2 | B | 256 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsB (rps2) |
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80371 | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S3 | C | 239 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsC (rps3) |
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80372 | ||||
Entity ID: 4 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S4 | D | 209 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsD (rps4) |
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80373 | ||||
Entity ID: 5 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S5 | E | 162 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsE |
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHQ5 | ||||
Entity ID: 6 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S6 | F | 101 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsF |
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SLP8 | ||||
Entity ID: 7 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S7 | G | 156 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsG (rps7) |
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P17291 | ||||
Entity ID: 8 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S8 | H | 138 | Thermus aquaticus | Mutation(s): 0 Gene Names: rpsH |
Find proteins for A0A0M9AFS9 (Thermus aquaticus) Go to UniProtKB: A0A0M9AFS9 | ||||
Entity ID: 9 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S9 | I | 128 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsI (rps9) |
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80374 | ||||
Entity ID: 10 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S10 | J | 105 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsJ |
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN7 | ||||
Entity ID: 11 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S11 | K | 129 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsK (rps11) |
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80376 | ||||
Entity ID: 12 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S12 | L | 135 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsL |
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHN3 | ||||
Entity ID: 13 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S13 | M | 126 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsM (rps13) |
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80377 | ||||
Entity ID: 14 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S14 | N | 61 | Thermus aquaticus | Mutation(s): 0 Gene Names: rpsZ (rpsN) |
Find proteins for A0A0N0BLP2 (Thermus aquaticus) Go to UniProtKB: A0A0N0BLP2 | ||||
Entity ID: 15 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S15 | O | 89 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsO |
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SJ76 | ||||
Entity ID: 16 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S16 | P | 88 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsP |
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SJH3 | ||||
Entity ID: 17 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S17 | Q | 105 | Thermus aquaticus | Mutation(s): 0 Gene Names: rpsQ |
Find proteins for A0A0N0BLS5 (Thermus aquaticus) Go to UniProtKB: A0A0N0BLS5 | ||||
Entity ID: 18 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S18 | R | 88 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsR |
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SLQ0 | ||||
Entity ID: 19 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S19 | S | 93 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsS |
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SHP2 | ||||
Entity ID: 20 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein S20 | T | 106 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsT (rps20) |
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: P80380 | ||||
Entity ID: 21 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| ribosomal protein THX | U | 27 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Mutation(s): 0 Gene Names: rpsU |
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB: Q5SIH3 | ||||
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Length | Organism | |
| 16S rRNA | A | 1522 | Thermus thermophilus HB8 | |
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | D, N | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
| MG Query on MG | A, B, C, D, E, F, J, M, P, Q, S | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 9 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PSU Query on PSU | A | RNA LINKING | C9 H13 N2 O9 P |  | U |
| 5MC Query on 5MC | A | RNA LINKING | C10 H16 N3 O8 P |  | C |
| M2G Query on M2G | A | RNA LINKING | C12 H18 N5 O8 P |  | G |
| MA6 Query on MA6 | A | RNA LINKING | C12 H18 N5 O7 P |  | A |
| 2MG Query on 2MG | A | RNA LINKING | C11 H16 N5 O8 P |  | G |
| UR3 Query on UR3 | A | RNA LINKING | C10 H15 N2 O9 P |  | U |
| 7MG Query on 7MG | A | RNA LINKING | C11 H18 N5 O8 P |  | G |
| 0TD Query on 0TD | L | L-PEPTIDE LINKING | C5 H9 N O4 S |  | ASP |
| 4OC Query on 4OC | A | RNA LINKING | C11 H18 N3 O8 P |  | C |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.853 Å
- R-Value Free: 0.206
- R-Value Work: 0.147
- Space Group: P 41 21 2
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 402.108 | α = 90.00 |
| b = 402.108 | β = 90.00 |
| c = 173.997 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| DENZO | data reduction |
| HKL-2000 | data collection |
| PHENIX | refinement |
| PHENIX | phasing |
Entry History
Deposition Data
- Deposited Date: 2012-02-22
- Released Date: 2013-02-27
- Deposition Author(s): Demirci, H., Murphy IV, F., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.
Revision History
- Version 1.0: 2013-02-27
Type: Initial release
