2QMO

Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.148

Literature

Macromolecules
Sequence Display for 2QMO

Classification: LIGASE

Total Structure Weight: 24888.10

Macromolecule Entities
Molecule Chains Length Organism Details
Dethiobiotin synthetase A 220 Helicobacter pylori EC#: 6.3.3.3 IUBMB
Mutation: M1M, M131M, M142M, M213M
Gene Name(s): bioD HP_0029
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 82.10 α = 90.00
b = 37.45 β = 101.48
c = 69.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-16
  • Released Date: 2007-07-31
  • Deposition author(s): Chruszcz, M., Xu, X., Cuff, M., Cymborowski, M., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update
  • 2012-03-28
    Type: Citation | Details: Citation update
  • 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