3P9Z

Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 3P9Z

Classification: LIGASE

Total Structure Weight: 26411.24

Macromolecule Entities
Molecule Chains Length Organism Details
Uroporphyrinogen III cosynthase (HemD) A 229 Helicobacter pylori Gene Name(s): HP_1224
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.202
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 55.41 α = 90.00
b = 57.68 β = 90.00
c = 74.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-18
  • Released Date: 2010-11-03
  • Deposition author(s): Nocek, B., Stein, A., Chhor, G., Fenske, R.J., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2010-11-03

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance