3R6D

Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine

Chang, C.Hatzos-Skintges, C.Clancy, S.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent epimerase/dehydratase221Veillonella parvula DSM 2008Mutation(s): 0 
Gene Names: Vpar_0111
UniProt
Find proteins for D1BQI7 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / CCUG 5123 / JCM 12972 / NCTC 11810 / Te3))
Explore D1BQI7 
Go to UniProtKB:  D1BQI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1BQI7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.446α = 90
b = 60.721β = 90
c = 69.612γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance