3R5F

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP

Doan, T.T.N.Kim, J.K.Kang, L.W.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanine--D-alanine ligase 1
A
384Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)Gene Names: ddlA (ddl)
EC: 6.3.2.4
Find proteins for Q5H614 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
Go to UniProtKB:  Q5H614
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.225α = 90.00
b = 83.225β = 90.00
c = 97.143γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance