3DB2

Crystal structure of a putative nadph-dependent oxidoreductase (dhaf_2064) from desulfitobacterium hafniense dcb-2 at 1.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.174 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of putative NADPH-dependent oxidoreductase (ZP_01370612.1) from DESULFITOBACTERIUM HAFNIENSE DCB-2 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative NADPH-dependent oxidoreductaseA, B, C354Desulfitobacterium hafniense DCB-2Mutation(s): 0 
Gene Names: ZP_01370612.1Dhaf_4026Dhaf_2064
UniProt
Find proteins for B8FRW3 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2))
Explore B8FRW3 
Go to UniProtKB:  B8FRW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8FRW3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth C],
E [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.616α = 90
b = 104.616β = 90
c = 173.372γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
PHENIXrefinement
SHELXphasing
SHELXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description