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 
• Deposition Author(s): Batuecas, M.T., Hermoso, J.A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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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

Literature

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem

Batuecas, M.T., Hermoso, J.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.87 kDa 
• Atom Count: 4,071 
• Modeled Residue Count: 490 
• Deposited Residue Count: 523 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase YcbB	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MXR (Subject of Investigation/LOI)	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	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Batuecas, M.T., Hermoso, J.A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2017-90030-P

Revision History  

• 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