2IM5 | pdb_00002im5

Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis

• PDB DOI: https://doi.org/10.2210/pdb2IM5/pdb

• Classification: TRANSFERASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-03 Released: 2006-10-24 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas gingivalis

Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 182.13 kDa 
• Atom Count: 13,047 
• Modeled Residue Count: 1,556 
• Deposited Residue Count: 1,576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate phosphoribosyltransferase	A, B, C, D	394	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: pncB EC: 6.3.4.21
UniProt
Find proteins for Q7MXV0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXV0  Go to UniProtKB:  Q7MXV0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.873	α = 90
b = 101.131	β = 90
c = 191.051	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-24 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references