2IGA

Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 2IGA

Classification: OXIDOREDUCTASE

Total Structure Weight: 169371.19

Macromolecule Entities
Molecule Chains Length Organism Details
Homoprotocatechuate 2,3-dioxygenase A, B, C, D 365 Brevibacterium fuscum EC#: 1.13.11.15 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XX3
Query on XX3

B, D (1S)-1-HYDROPEROXY-1-HYDROXY-2-KETO-5-NITROCYCLOHEXA- 3,5-DIENE
C6 H5 N O6
FWUJUIQFDWUIAR-LURJTMIESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XXP
Query on XXP

A 2-KETO,5-NITRO,6-HYDROXY-3,5-HEXADIENOIC ACID
C6 H5 N O6
UDOBAQIWFWMQMT-BXTBVDPRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XX2
Query on XX2

C 1-KETO,2-HYDROXY,4-NITROBENZENE, 1 ELECTRON OXIDIZED
C6 H4 N O4
KJBVYJMPBKCQJZ-ZCFIWIBFBW
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, B, C, D FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXY
Query on OXY

C OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.185
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 110.68 α = 90.00
b = 153.02 β = 90.00
c = 96.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-09-22
  • Released Date: 2007-04-24
  • Deposition author(s): Kovaleva, E.G., Lipscomb, J.D.

Revision History

  • Version 1_0: 2007-04-24

    Type: Initial release

  • Version 1_1: 2007-10-16

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance