Download MendeleyCrystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3
Arai, R., Ito, K., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S.To be published.
2CZ5
Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus horikoshii OT3
- PDB DOI: https://doi.org/10.2210/pdb2CZ5/pdb
- Classification: LYASE
- Organism(s): Pyrococcus horikoshii
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-07-11 Released: 2006-01-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.231
- R-Value Work: 0.193
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Orotidine 5'-phosphate decarboxylase | 208 | Pyrococcus horikoshii | Mutation(s): 0 Gene Names: pyrF, PH0731 EC: 4.1.1.23 |  | |
UniProt | |||||
Find proteins for O58462 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58462 Go to UniProtKB: O58462 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O58462 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | C [auth A], D [auth B] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | E [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.231
- R-Value Work: 0.193
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 44.427 | α = 90 |
| b = 59.909 | β = 90 |
| c = 152.519 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2006-01-11 Deposition Author(s): Arai, R., Ito, K., Kamo-Uchikubo, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2006-01-11
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
