1KNF

Crystal Structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase Complexed with 3-methyl Catechol under Anaerobic Condition

Structural Biology Knowledgebase: 1KNF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 1KNF

Classification: OXIDOREDUCTASE

Total Structure Weight: 32761.90

Macromolecule Entities
Molecule Chains Length Organism Details
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE A 297 Paraburkholderia xenovorans EC#: 1.13.11.39 IUBMB
Gene Name(s): bphC Bxeno_C1125 Bxe_C1191
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MBD
Query on MBD

A 3-METHYLCATECHOL
2-DIOL, (Synonym)
C7 H8 O2
PGSWEKYNAOWQDF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TBU
Query on TBU

A TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL (Synonym)
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.168
  • Space Group: I 4 2 2

Unit Cell:

Length (Å) Angle (°)
a = 123.10 α = 90.00
b = 123.10 β = 90.00
c = 110.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-18
  • Released Date: 2002-03-27
  • Deposition author(s): Han, S., Bolin, J.T.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4