Download MendeleyCrystal structures and kinetic properties of anabolic ornithine carbamoyltransferase from human pathogens Vibrio vulnificus and Bacillus anthracis
Shabalin, I.G., Winsor, J., Grimshaw, S., Minor, W.To be published.
4JHX
Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoylphosphate and arginine
- PDB DOI: https://doi.org/10.2210/pdb4JHX/pdb
- Classification: TRANSFERASE
- Organism(s): Vibrio vulnificus CMCP6
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-03-05 Released: 2013-03-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.190
- R-Value Work: 0.154
- R-Value Observed: 0.156
Starting Model: experimental
View more details
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 |
| Ornithine carbamoyltransferase | 358 | Vibrio vulnificus CMCP6 | Mutation(s): 0 Gene Names: argF, VV1_1466 EC: 2.1.3.3 |  | |
UniProt | |||||
Find proteins for Q8DCF5 (Vibrio vulnificus (strain CMCP6)) Explore Q8DCF5 Go to UniProtKB: Q8DCF5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8DCF5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ARG Query on ARG | F [auth A] | ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O |  | ||
| CP Query on CP | D [auth A], K [auth C] | PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | I [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A], G [auth B], H [auth B], J [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.190
- R-Value Work: 0.154
- R-Value Observed: 0.156
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/m3388n
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 76.029 | α = 90 |
| b = 79.387 | β = 90 |
| c = 147.169 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| MOLREP | phasing |
| CCP4 | phasing |
Entry History
Deposition Data
- Released Date: 2013-03-20 Deposition Author(s): Shabalin, I.G., Bacal, P., Winsor, J., Grimshaw, S., Grabowski, M., Chordia, M.D., Shuvalova, L., Anderson, W.F., Minor, W., 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: 2022-04-13
Changes: Database references, Derived calculations, Structure summary - Version 1.2: 2023-09-20
Changes: Data collection, Refinement description
