3QXJ

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 3QXJ

Classification: LIGASE

Total Structure Weight: 28316.19

Macromolecule Entities
Molecule Chains Length Organism Details
Dethiobiotin synthetase A 242 Helicobacter pylori EC#: 6.3.3.3 IUBMB
Gene Name(s): bioD HP_0029
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GTP
Query on GTP

A GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-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: 1.38 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.159
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 82.15 α = 90.00
b = 37.50 β = 101.23
c = 69.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-01
  • Released Date: 2011-03-30
  • Deposition author(s): Klimecka, M.M., Porebski, P.J., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2011-03-30

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2012-03-28

    Type: Database references

  • Version 1_3: 2013-03-27

    Type: Database references