7AJ9

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae

Batuecas, M.T.Hermoso, J.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L,D-transpeptidase YcbBA, B523Vibrio choleraeMutation(s): 0 
Gene Names: ERS013138_01558ERS013186_00077ERS013206_00149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.92α = 90
b = 93.046β = 90
c = 249.983γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

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