Download MendeleyCrystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.
Shahid, S., Kabra, A., Pal, R.K., Arora, A.To be published.
5GVZ
Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.
- PDB DOI: https://doi.org/10.2210/pdb5GVZ/pdb
- Classification: HYDROLASE
- Organism(s): Vibrio cholerae O395
- Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
- Mutation(s): No
- Deposited: 2016-09-07 Released: 2017-09-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.235
- R-Value Work: 0.191
- R-Value Observed: 0.193
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Peptidyl-tRNA hydrolase | 197 | Vibrio cholerae O395 | Mutation(s): 0 Gene Names: pth, VC0395_A1761, VC395_2298 EC: 3.1.1.29 |  | |
UniProt | |||||
Find proteins for A5F686 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F686 Go to UniProtKB: A5F686 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A5F686 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACT Query on ACT | C [auth A], D [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 2CO Query on 2CO | A | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.235
- R-Value Work: 0.191
- R-Value Observed: 0.193
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.136 | α = 90 |
| b = 73.462 | β = 90 |
| c = 120.52 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2017-09-20 Deposition Author(s): Shahid, S., Kabra, A., Pal, R.K., Arora, A.
Revision History (Full details and data files)
- Version 1.0: 2017-09-20
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description
