3P9Z | pdb_00003p9z

Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695

• PDB DOI: https://doi.org/10.2210/pdb3P9Z/pdb

• Classification: LIGASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-18 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.241 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695

Nocek, B., Stein, A., Chhor, G., Fenske, R.J., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.41 kDa 
• Atom Count: 1,815 
• Modeled Residue Count: 213 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uroporphyrinogen III cosynthase (HemD)	A	229	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_1224 EC: 4.2.1.75
UniProt
Find proteins for O25822 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25822  Go to UniProtKB:  O25822

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.241 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.407	α = 90
b = 57.676	β = 90
c = 74.624	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary