3OJC

Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis

Anderson, S.M.Wawrzak, Z.Kudritska, M.Kwon, K.Anderson, W.F.Savchenko, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative aspartate/glutamate racemaseA, B, C, D231Yersinia pestis CO92Mutation(s): 0 
Gene Names: racXYPO2758YP_2405
EC: 5.1.1.13
Find proteins for A0A2S9PI63 (Yersinia pestis)
Explore A0A2S9PI63 
Go to UniProtKB:  A0A2S9PI63
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , H [auth A] , I [auth A] , J [auth A] , L [auth B] , M [auth B] , N [auth B] , 
AA [auth D],  BA [auth D],  H [auth A],  I [auth A],  J [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth C],  U [auth C],  V [auth C],  W [auth C],  X [auth C],  Y [auth D],  Z [auth D]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], K [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.52α = 90
b = 95.41β = 90
c = 142.62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-11-08
    Changes: Refinement description