Download MendeleyCrystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3BF5
Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3BF5/pdb
- Classification: TRANSFERASE
- Organism(s): Thermoplasma acidophilum DSM 1728
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-11-20 Released: 2007-12-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.245
- R-Value Work: 0.202
- R-Value Observed: 0.205
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ribokinase related protein | 306 | Thermoplasma acidophilum DSM 1728 | Mutation(s): 3 Gene Names: 10640157, Ta0880 EC: 2.7.1.213 (UniProt), 2.7.1.20 (UniProt), 2.7.1.73 (UniProt) |  | |
UniProt | |||||
Find proteins for Q9HJT3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJT3 Go to UniProtKB: Q9HJT3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HJT3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | F [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| PGO Query on PGO | C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] | S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.245
- R-Value Work: 0.202
- R-Value Observed: 0.205
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M33BF5
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.45 | α = 90 |
| b = 59.18 | β = 90 |
| c = 177.65 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2007-12-04 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-12-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2021-10-20
Changes: Database references, Derived calculations - Version 1.5: 2023-01-25
Changes: Database references
