Download Mendeley2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630
Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F.To be published.
4JJP
2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630
- PDB DOI: https://doi.org/10.2210/pdb4JJP/pdb
- Classification: TRANSFERASE
- Organism(s): Clostridioides difficile 630
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-03-08 Released: 2013-03-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.06 Å
- R-Value Free: 0.218
- R-Value Work: 0.181
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Phosphomethylpyrimidine kinase | 267 | Clostridioides difficile 630 | Mutation(s): 0 Gene Names: CD630_15990, thiD EC: 2.7.4.7 |  | |
UniProt | |||||
Find proteins for Q186F5 (Clostridioides difficile (strain 630)) Explore Q186F5 Go to UniProtKB: Q186F5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q186F5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | C [auth B] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.06 Å
- R-Value Free: 0.218
- R-Value Work: 0.181
- R-Value Observed: 0.183
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M34JJP
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.751 | α = 90 |
| b = 79.741 | β = 90 |
| c = 92.863 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Blu-Ice | data collection |
| BALBES | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2013-03-20 Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2013-03-20
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description - Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
