7AJZ

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with NAG-NAM(tetrapeptide)


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
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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L,D-transpeptidase YcbB
A, B
523Vibrio choleraeMutation(s): 0 
Gene Names: ERS013138_01558ERS013186_00077ERS013206_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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KSI8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAG-NAM(tetrapeptide)4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
API
Query on API
C
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
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 = 57.51α = 90
b = 92.558β = 90
c = 276.064γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2017-90030-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