Download MendeleyCrystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate
Vance, N.R., Spies, M.A.To be published.
5W1Q
Crystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate
- PDB DOI: https://doi.org/10.2210/pdb5W1Q/pdb
- Classification: ISOMERASE
- Organism(s): Helicobacter pylori
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-06-04 Released: 2017-06-21
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.228
- R-Value Work: 0.168
- R-Value Observed: 0.171
Starting Model: experimental
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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 |
| Glutamate racemase | 275 | Helicobacter pylori | Mutation(s): 0 Gene Names: murI, OUM_0701 EC: 5.1.1.3 |  | |
UniProt | |||||
Find proteins for K2K6A3 (Helicobacter pylori R038b) Explore K2K6A3 Go to UniProtKB: K2K6A3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | K2K6A3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGL Query on DGL | C [auth A], F [auth B] | D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N |  | ||
| GOL Query on GOL | D [auth A], E [auth A], G [auth B], H [auth B], I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.228
- R-Value Work: 0.168
- R-Value Observed: 0.171
- Space Group: P 2 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 61.878 | α = 90 |
| b = 85.555 | β = 90 |
| c = 105.989 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-06-21 Deposition Author(s): Vance, N.R., Spies, M.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM097373 |
Revision History (Full details and data files)
- Version 1.0: 2017-06-21
Type: Initial release - Version 1.1: 2017-09-13
Changes: Author supporting evidence - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
