Download MendeleyThe crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
Wu, R., James, A., Joachimiak, A.To be published.
2P7J | pdb_00002p7j
Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
- PDB DOI: https://doi.org/10.2210/pdb2P7J/pdb
- Classification: TRANSCRIPTION
- Organism(s): Vibrio parahaemolyticus RIMD 2210633
- Expression System: Escherichia coli BL21
- Mutation(s): Yes
- Deposited: 2007-03-20 Released: 2007-05-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.239 (Depositor), 0.237 (DCC)
- R-Value Work: 0.193 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.196 (Depositor)
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 |
| Putative sensory box/GGDEF family protein | 287 | Vibrio parahaemolyticus RIMD 2210633 | Mutation(s): 3 Gene Names: VP0354 EC: 2.7.7.65 |  | |
UniProt | |||||
Find proteins for Q87SR8 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87SR8 Go to UniProtKB: Q87SR8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q87SR8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A], E [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACY Query on ACY | F [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| NA Query on NA | D [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.239 (Depositor), 0.237 (DCC)
- R-Value Work: 0.193 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.196 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.98 | α = 90 |
| b = 81.596 | β = 90 |
| c = 121.851 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
Entry History
Deposition Data
- Released Date: 2007-05-01 Deposition Author(s): Wu, R., James, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-05-01
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
