7AJZ | pdb_00007ajz

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 
• 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: 2.98 Å
• R-Value Free: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

The 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.6 kDa 
• Atom Count: 7,978 
• Modeled Residue Count: 979 
• Deposited Residue Count: 1,050 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase YcbB	A, B	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAG-NAM(tetrapeptide)	C	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMV (Subject of Investigation/LOI)	F [auth C]	methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside C12 H21 N O8 UXEQYDNCHCKBIL-PKKPQKKZSA-N
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	C	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
DAL	C	D-PEPTIDE LINKING	C3 H7 N O2		--
DGL	C	D-PEPTIDE LINKING	C5 H9 N O4		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

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 Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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 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