Download MendeleyCrystal structure of unknown function protein VPA0580.
Chang, C., Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A.To be published.
2QHQ | pdb_00002qhq
Crystal structure of unknown function protein VPA0580
- PDB DOI: https://doi.org/10.2210/pdb2QHQ/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Vibrio parahaemolyticus RIMD 2210633
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-07-02 Released: 2007-07-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.76 Å
- R-Value Free: 0.209 (Depositor), 0.207 (DCC)
- R-Value Work: 0.170 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.172 (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 |
| Unknown function protein VPA0580 | 125 | Vibrio parahaemolyticus RIMD 2210633 | Mutation(s): 10 Gene Names: VPA0580 |  | |
UniProt | |||||
Find proteins for Q87IM6 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87IM6 Go to UniProtKB: Q87IM6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q87IM6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACT Query on ACT | C [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MLY Query on MLY | A, B | L-PEPTIDE LINKING | C8 H18 N2 O2 |  | LYS |
| 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: 1.76 Å
- R-Value Free: 0.209 (Depositor), 0.207 (DCC)
- R-Value Work: 0.170 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.172 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 34.796 | α = 90 |
| b = 80.851 | β = 90 |
| c = 87.774 | 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: 2007-07-17 Deposition Author(s): Chang, C., Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-07-17
Type: Initial release - Version 1.1: 2007-11-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary
