Download MendeleyThe X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)
Batuecas, M.T., Hermoso, J.A.To be published.
7AJZ
The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)
- PDB DOI: https://doi.org/10.2210/pdb7AJZ/pdb
- Classification: TRANSFERASE
- Organism(s): Vibrio cholerae, synthetic construct
- 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: 2.98 Å
- R-Value Free: 0.266
- R-Value Work: 0.209
- R-Value Observed: 0.212
Starting Model: experimental
View more details
This is version 3.1 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 |
| 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 | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAG-NAM(tetrapeptide) | 4 | synthetic construct | Mutation(s): 0 |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AMV (Subject of Investigation/LOI) Query on AMV | F [auth C] | methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside C12 H21 N O8 UXEQYDNCHCKBIL-PKKPQKKZSA-N |  | ||
| EDO Query on EDO | D [auth A], E [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| API Query on API | C | L-PEPTIDE LINKING | C7 H14 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.98 Å
- R-Value Free: 0.266
- R-Value Work: 0.209
- R-Value Observed: 0.212
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.51 | α = 90 |
| b = 92.558 | β = 90 |
| c = 276.064 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| 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 2.0: 2022-12-21
Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary - Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations, Refinement description - Version 3.1: 2024-01-31
Changes: Refinement description
