3TC1 | pdb_00003tc1

Crystal Structure of Octaprenyl Pyrophosphate Synthase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb3TC1/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-08 Released: 2011-08-31 
• Deposition Author(s): Zhang, J.Y., Zhang, X.L., Li, D.F., Zou, Q.M., Wang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal Structure of Octaprenyl Pyrophosphate Synthase from Helicobacter pylori

Zhang, J.Y., Zhang, X.L., Li, D.F., Zou, Q.M., Wang, D.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 72.31 kDa 
• Atom Count: 5,296 
• Modeled Residue Count: 594 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaprenyl Pyrophosphate Synthase	A, B	315	Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093	Mutation(s): 0  Gene Names: HP0240
UniProt
Find proteins for O25023 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25023  Go to UniProtKB:  O25023

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.33	α = 90
b = 109.33	β = 90
c = 103.41	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Zhang, J.Y., Zhang, X.L., Li, D.F., Zou, Q.M., Wang, D.C.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2011-11-09
  Changes: Advisory, Data collection
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations