4EGJ

Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L.Gallagher, L.A.Patrapuvich, R.Clifton, M.C.Gardberg, A.S.Edwards, T.E.Armour, B.Begley, D.W.Dieterich, S.H.Dranow, D.M.Abendroth, J.Fairman, J.W.Fox, D.Staker, B.L.Phan, I.Gillespie, A.Choi, R.Nakazawa-Hewitt, S.Nguyen, M.T.Napuli, A.Barrett, L.Buchko, G.W.Stacy, R.Myler, P.J.Stewart, L.J.Manoil, C.Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanine--D-alanine ligase
A, B, C, D
334Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: Bxeno_A3907Bxe_A0488ddl
EC: 6.3.2.4
UniProt
Find proteins for Q13TZ4 (Paraburkholderia xenovorans (strain LB400))
Explore Q13TZ4 
Go to UniProtKB:  Q13TZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13TZ4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 43
  • Diffraction Data: https://doi.org/10.18430/M34EGJ
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.93α = 90
b = 78.93β = 90
c = 224.74γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHASERphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description