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Structure of IDP01976

2.1 Angstrom resolution crystal structure of glycerol-3-phosphate dehydrogenase (gpsA) from Coxiella burnetii.

Edit deposit information
CSGID target
IDP01976 
PDB Id
3K96 (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,S.N.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Oct 15, 2009 
Release Date
Oct 27, 2009 

Annotation

Description
Glycerol-3-phosphate dehydrogenase is an NADH dependent enzyme which catalyzes the reduction of dihydroxyacetone to glycerol-3-phosphate. The enzyme has variety of biological functions, including maintenance of the NADH/NAD+ balance, a role in glucose glycolysis pathway, and prevention of build-up of the toxic compound methylglyoxylate. The Coxiella burnetii enzyme’s biological homodimer is observed within the crystal’s asymmetric unit. Each monomer consists of and N-terminal NAD-binding domain and a C-terminal substrate-binding domain. While the enzyme is structurally similar to previously characterized homologs (PDB code 1N1E), one difference from some homologs is the truncation of the C-terminus. In homologs, the C-terminus is observed to form a portion of the dimer interface. The absence of these residues in the Coxiella burnetii enzyme results in a reduced protein-protein interactions.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
EPE
BME

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=85.27Å, b=88.45Å, c=97.29Å
α=90.00, β=90.00, γ=90.00 
Solvent content
47.9  
Matthews coefficient
2.36  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.27-2.10Å (2.15-2.10Å)  
Rall(%)
16.7 
Rwork(%)
16.4 (19.8) 
Rfree(%)
21.0 (27.4) 
Num. observed reflections
43577 (3195) 
Num. Rfree reflections
2178 (168) 
Completeness(%)
99.9 (100.0) 

Model parameters

Num Atoms
5188  
Num Waters
481  
Num Hetatoms
527  
Model mean isotropic B factor
28.020Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.388°  
Filename uploaded
rcsb055703.pdb (uploaded on Oct 16, 2009 3:35 PM)  
Inserted
Oct 16, 2009