1L3J

Crystal Structure of Oxalate Decarboxylase Formate Complex

Structural Biology Knowledgebase: 1L3J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 1L3J

Classification: METAL BINDING PROTEIN

Total Structure Weight: 43847.61

Macromolecule Entities
Molecule Chains Length Organism Details
YVRK PROTEIN A 385 Bacillus subtilis EC#: 4.1.1.2 IUBMB
Gene Name(s): oxdC yvrK BSU33240
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 0.193
  • R-Value Work: 0.169
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.80 α = 90.00
b = 154.80 β = 90.00
c = 122.16 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-27
  • Released Date: 2002-07-03
  • Deposition author(s): Anand, R., Dorrestein, P.C., Kinsland, C., Begley, T.P., Ealick, S.E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values