1YBE | pdb_00001ybe

Crystal Structure of a Nicotinate phosphoribosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb1YBE/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-20 Released: 2005-01-11 
• Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal Structure of a Nicotinate phosphoribosyltransferase

Seetharaman, J., Swaminathan, S.

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.

Macromolecule Content 

• Total Structure Weight: 103.28 kDa 
• Atom Count: 6,910 
• Modeled Residue Count: 832 
• Deposited Residue Count: 898 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate phosphoribosyltransferase	A, B	449	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: pncB EC: 2.4.2.11 (PDB Primary Data), 6.3.4.21 (UniProt)
UniProt
Find proteins for Q8UIS9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8UIS9  Go to UniProtKB:  Q8UIS9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.768	α = 90
b = 69.428	β = 90
c = 87.99	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Seetharaman, J., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-04-30
  Changes: Data collection
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references