3VB0

Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a dibenzofuran-degrading dioxygenase: an unusual spatially heterogeneous crystal with a hypersymmetric intensity distribution

Koksal, M.Kumar, P.Fortin, P.D.Eltis, L.D.Bolin, J.T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyoxalase/bleomycin resistance protein/dioxygenaseABCD294Sphingomonas wittichii RW1Mutation(s): 0 
Gene Names: dbfBSwit_4902
EC: 1.13.11
Find proteins for A5VGW5 (Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273))
Explore A5VGW5 
Go to UniProtKB:  A5VGW5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download CCD File 
A, B
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.587α = 90
b = 131.587β = 90
c = 103.146γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description