Download MendeleyThe crystal structure of D-alanyl-alanine synthetase A from Vibrio cholerae O1 biovar eltor str. N16961
Tan, K., Zhou, M., Joachimiak, A.To be published.
6DGI
The crystal structure of D-alanyl-alanine synthetase A from Vibrio cholerae O1 biovar eltor str. N16961
- PDB DOI: https://doi.org/10.2210/pdb6DGI/pdb
- Classification: LIGASE
- Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-05-17 Released: 2018-05-30
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.219
- R-Value Work: 0.177
- R-Value Observed: 0.179
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 |
| D-alanine--D-alanine ligase | 337 | Vibrio cholerae O1 biovar El Tor str. N16961 | Mutation(s): 0 Gene Names: ddl, VC_A0572 EC: 6.3.2.4 |  | |
UniProt | |||||
Find proteins for Q9KM17 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KM17 Go to UniProtKB: Q9KM17 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KM17 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | C [auth A], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | D [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| MG Query on MG | E [auth A], G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.30 Å
- R-Value Free: 0.219
- R-Value Work: 0.177
- R-Value Observed: 0.179
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.588 | α = 90 |
| b = 64.875 | β = 90 |
| c = 165.16 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-05-30 Deposition Author(s): Tan, K., Zhou, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201700060C |
Revision History (Full details and data files)
- Version 1.0: 2018-05-30
Type: Initial release - Version 1.1: 2019-12-18
Changes: Author supporting evidence
