Download MendeleyCRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.To be published.
5D8H
CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
- PDB DOI: https://doi.org/10.2210/pdb5D8H/pdb
- NAKB: 5D8H
- Classification: RIBOSOMAL PROTEIN
- Organism(s): Methanocaldococcus jannaschii, Streptomyces azureus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2015-08-17 Released: 2016-08-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.245
- R-Value Work: 0.208
- R-Value Observed: 0.210
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 50S ribosomal protein L10 | 213 | Methanocaldococcus jannaschii | Mutation(s): 1 Gene Names: rpl10, rplP0, MJ0509 |  | |
UniProt | |||||
Find proteins for P54049 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54049 Go to UniProtKB: P54049 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P54049 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 50S ribosomal protein L11 | 161 | Methanocaldococcus jannaschii | Mutation(s): 0 Gene Names: rpl11, MJ0373 |  | |
UniProt | |||||
Find proteins for P54030 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54030 Go to UniProtKB: P54030 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P54030 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| THIOSTREPTON | 19 | Streptomyces azureus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P0C8P8 (Streptomyces azureus) Explore P0C8P8 Go to UniProtKB: P0C8P8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0C8P8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 23S ribosomal RNA | 74 | Methanocaldococcus jannaschii |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | R [auth A], S [auth A], U [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| MG Query on MG | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | O [auth A], P [auth A], Q [auth A], T [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
| BB9 Query on BB9 | D | PEPTIDE LINKING | C3 H5 N O2 S |  | CYS |
| DBU Query on DBU | D | PEPTIDE LINKING | C4 H7 N O2 |  | THR |
| DHA Query on DHA | D | PEPTIDE LINKING | C3 H5 N O2 |  | SER |
| MH6 Query on MH6 | D | PEPTIDE LINKING | C3 H5 N O3 |  | SER |
| TS9 Query on TS9 | D | L-PEPTIDE LINKING | C6 H13 N O4 |  | ILE |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000223 Query on PRD_000223 | D | THIOSTREPTON | Thiopeptide / Antibiotic |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.245
- R-Value Work: 0.208
- R-Value Observed: 0.210
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 125.07 | α = 90 |
| b = 127.16 | β = 90 |
| c = 132.93 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2016-08-24 Deposition Author(s): Gabdulkhakov, A.G., Mitroshin, I.V., Garber, M.B.
Revision History (Full details and data files)
- Version 1.0: 2016-08-24
Type: Initial release - Version 1.1: 2016-12-14
Changes: Structure summary - Version 1.2: 2016-12-21
Changes: Non-polymer description - Version 1.3: 2019-04-10
Changes: Advisory, Data collection, Database references - Version 2.0: 2019-04-24
Changes: Data collection, Polymer sequence
