Download MendeleyThe X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem
Batuecas, M.T., Hermoso, J.A.To be published.
7AJX | pdb_00007ajx
The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem
- PDB DOI: https://doi.org/10.2210/pdb7AJX/pdb
- Classification: TRANSFERASE
- Organism(s): Vibrio cholerae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-09-29 Released: 2021-10-06
- Funding Organization(s): Spanish Ministry of Economy and Competitiveness
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.267 (Depositor), 0.270 (DCC)
- R-Value Work: 0.209 (Depositor), 0.220 (DCC)
Starting Model: experimental
View more details
This is version 1.2 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 |
| L,D-transpeptidase YcbB | 523 | Vibrio cholerae | Mutation(s): 0 Gene Names: ERS013138_01558, ERS013186_00077, ERS013206_00149 |  | |
UniProt | |||||
Find proteins for Q9KSI8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KSI8 Go to UniProtKB: Q9KSI8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9KSI8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MXR (Subject of Investigation/LOI) Query on MXR | B [auth A] | (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-DKLFCYGSSA-N |  | ||
| EDO Query on EDO | C [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.267 (Depositor), 0.270 (DCC)
- R-Value Work: 0.209 (Depositor), 0.220 (DCC)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.877 | α = 90 |
| b = 101.224 | β = 90 |
| c = 115.285 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-10-06 Deposition Author(s): Batuecas, M.T., Hermoso, J.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Spanish Ministry of Economy and Competitiveness | Spain | BFU2017-90030-P |
Revision History (Full details and data files)
- Version 1.0: 2021-10-06
Type: Initial release - Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description - Version 1.2: 2024-11-13
Changes: Structure summary
