3V4Z

D-alanine--D-alanine ligase from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

D-alanine--D-alanine ligase from Yersinia pestis.

Osipiuk, J.Nocek, B.Mulligan, R.Papazisi, L.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanine--D-alanine ligase
A, B
309Yersinia pestisGene Names: ddl (ddlB)
EC: 6.3.2.4
Find proteins for Q8ZIE7 (Yersinia pestis)
Go to UniProtKB:  Q8ZIE7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 100.637α = 90.00
b = 100.637β = 90.00
c = 110.304γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-3000phasing
HKL-3000data reduction
REFMACrefinement
HKL-3000data scaling
SCALEPACKdata scaling
MOLREPphasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description