2B1X

Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.

Structural Biology Knowledgebase: 2B1X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 2B1X

Classification: OXIDOREDUCTASE

Total Structure Weight: 219485.05

Macromolecule Entities
Molecule Chains Length Organism Details
naphthalene dioxygenase large subunit A, C, E 470 Rhodococcus sp. ncimb12038 EC#: 1.14.12.12 IUBMB
Gene Name(s): narAa
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
naphthalene dioxygenase small subunit B, D, F 172 Rhodococcus sp. ncimb12038 EC#: 1.14.12.12 IUBMB
Gene Name(s): narAb
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C, E FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, C, E (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, C, E FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.191
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 87.74 α = 90.00
b = 144.25 β = 90.00
c = 186.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-09-16
  • Released Date: 2005-10-04
  • Deposition author(s): Gakhar, L., Malik, Z.A., Allen, C.C., Lipscomb, D.A., Larkin, M.J., Ramaswamy, S.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 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