Download MendeleyCrystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)
Joint Center for Structural Genomics (JCSG)To be published.
3MBH | pdb_00003mbh
Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)
- PDB DOI: https://doi.org/10.2210/pdb3MBH/pdb
- Classification: TRANSFERASE
- Organism(s): Bacteroides thetaiotaomicron VPI-5482
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-03-25 Released: 2010-06-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.206 (Depositor), 0.220 (DCC)
- R-Value Work: 0.167 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.169 (Depositor)
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 |
| Putative phosphomethylpyrimidine kinase | 291 | Bacteroides thetaiotaomicron VPI-5482 | Mutation(s): 0 Gene Names: BT_4458 EC: 2.7.1.35 |  | |
UniProt | |||||
Find proteins for Q89ZB9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZB9 Go to UniProtKB: Q89ZB9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q89ZB9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PXL Query on PXL | G [auth A] I [auth B] J [auth C] L [auth D] M [auth E] | 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE C8 H9 N O3 RADKZDMFGJYCBB-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth A], K [auth C], N [auth E], P [auth F] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D, E A, B, C, D, E, F | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.206 (Depositor), 0.220 (DCC)
- R-Value Work: 0.167 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.169 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33MBH
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 93.723 | α = 90 |
| b = 138.368 | β = 90 |
| c = 143.539 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2010-06-02 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-06-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-27
Changes: Data collection, Refinement description, Structure summary
