Download MendeleyCrystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis
Agarwal, R., Burley, S.K., Swaminathan, S.To be published.
2PBZ
Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis
- PDB DOI: https://doi.org/10.2210/pdb2PBZ/pdb
- Classification: LIGASE
- Organism(s): Thermococcus kodakarensis KOD1
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-03-29 Released: 2007-04-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.300
- R-Value Work: 0.276
- R-Value Observed: 0.276
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 |
| Hypothetical protein | 320 | Thermococcus kodakarensis KOD1 | Mutation(s): 3 Gene Names: PurP, TK0431 EC: 6.3.4 |  | |
UniProt | |||||
Find proteins for Q5JD28 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JD28 Go to UniProtKB: Q5JD28 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5JD28 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | D [auth A], E [auth B], F [auth C] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.300
- R-Value Work: 0.276
- R-Value Observed: 0.276
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.342 | α = 90 |
| b = 87.4 | β = 90 |
| c = 175.907 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHARP | phasing |
| SHELXD | phasing |
Entry History
Deposition Data
- Released Date: 2007-04-10 Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2007-04-10
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
