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Structure of IDP90669

2.00 Angstrom resolution crystal structure of a quinolinate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961

Edit deposit information
CSGID target
IDP90669 
PDB Id
3PAJ (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,J.Winsor,I.Dubrovska,L.Shuvalova,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Oct 19, 2010 
Release Date
Nov 03, 2010 

Annotation

Description
Quinolinate phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) catalyzes the formation of nicotinate mononucleotide, carbon dioxide, and pyrophosphate from 5-phosphoribosyl 1-pyrophosphate (PRPP) and quinolinic acid (QA, pyridine 2,3-dicarboxylic acid). The 2.0 A resolution crystal structure of apo-QAPRTase is a two-domain enzyme, which forms a dimer with the buried surface area of 4970 A2 in the crystal. In each chain, smaller bridging alpha/beta N-terminal domain and bigger TIM-barrel C-terminal domain are interconnected by a ~50 A long alpha helix. The C-terminal half of this helix represents the first helix in the TIM-barrel structure. The N-terminal domain resembles the Rossmann fold and covers the active site of the TIM-barrel part of the V. cholerae apo-QAPRTase.  
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=59.20Å, b=79.55Å, c=117.91Å
α=90.00, β=90.00, γ=90.00 
Solvent content
38.27  
Matthews coefficient
1.99  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.60-2.00Å (2.05-2.00Å)  
Rall(%)
17.6 
Rwork(%)
17.3 (16.6) 
Rfree(%)
22.2 (21.8) 
Num. observed reflections
38067 (2691) 
Num. Rfree reflections
1903 (154) 
Completeness(%)
99.7 (98.5) 

Model parameters

Num Atoms
4736  
Num Waters
414  
Num Hetatoms
422  
Model mean isotropic B factor
26.540Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.609°  
Filename uploaded
3PAJ.pdb (uploaded on Sep 28, 2011 11:17 AM)  
Inserted
Oct 29, 2010