2B7Q | pdb_00002b7q

Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori with nicotinate mononucleotide

• PDB DOI: https://doi.org/10.2210/pdb2B7Q/pdb

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


• Deposited: 2005-10-05 Released: 2006-02-21 
• Deposition Author(s): Kim, M.K., Im, Y.J., Lee, J.H., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 
  0.286 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori

Kim, M.K., Im, Y.J., Lee, J.H., Eom, S.H.

(2006) Proteins 63: 252-255

• PubMed: 16419067 
• DOI: https://doi.org/10.1002/prot.20834
• Primary Citation Related Structures: 
  2B7N, 2B7P, 2B7Q

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Organizational Affiliation: 
• Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, South Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 93.56 kDa 
• Atom Count: 6,564 
• Modeled Residue Count: 819 
• Deposited Residue Count: 819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide pyrophosphorylase	A, B, C	273	Helicobacter pylori	Mutation(s): 0  EC: 2.4.2.19
UniProt
Find proteins for O25909 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25909  Go to UniProtKB:  O25909

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCN	D [auth A], E [auth B], F [auth C]	NICOTINATE MONONUCLEOTIDE C11 H14 N O9 P JOUIQRNQJGXQDC-ZYUZMQFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free:  0.286 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.855	α = 90
b = 148.855	β = 90
c = 145.662	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
AUTOMAR	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-21 
Deposition Author(s): Kim, M.K., Im, Y.J., Lee, J.H., Eom, S.H.

Revision History  

• Version 1.0: 2006-02-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-09-19
  Changes: Data collection, Structure summary
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations