Structure of IDP91419

2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6

Edit deposit information
CSGID target
IDP91419 
PDB Id
4E0B (NCBI MMDB
Authors
A.S.Halavaty,Z.Wawrzak,O.Onopriyenko,K.Kwon,W.F.Anderson,A.Savchenko,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Mar 02, 2012 
Release Date
Mar 21, 2012 

Annotation

Description
Malate dehydrogenase (MDH) is an enzyme of the citric acid cycle that catalyzes the reversible oxidation of malate to oxaloacetate with the concomitant reduction of NADH. The 2.17 Å resolution crystal structure of the malate dehydrogenase from Vibrio vulnificus CMCP6 was determined by molecular replacement using the structure of the malate dehydrogenase from Escherichia coli (PDB code 3HHP) as a model. The asymmetric unit has four molecules that form two dimmers with the total buried surface area of 3,570 Å2. The protein exhibits an α/β fold with the presence of the Rossman fold sitting at the dimerization interface. The active site loop (residues 81 through 86) in all four subunits is disordered.  
Functional assignment
OXIDOREDUCTASE 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=79.04Å, b=80.76Å, c=99.43Å
α=90.00, β=109.42, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.20-2.17Å (2.23-2.17Å)  
Rall(%)
16.5 
Rwork(%)
16.3 (21.2) 
Rfree(%)
20.7 (26.6) 
Num. observed reflections
62458 (4578) 
Num. Rfree reflections
3122 (259) 
Completeness(%)
99.8 (100.0) 

Model parameters

Num Atoms
8924  
Num Waters
709  
Num Hetatoms
847  
Model mean isotropic B factor
34.210Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.270°  
Filename uploaded
4E0B.pdb (uploaded on Apr 16, 2012 2:20 PM)  
Inserted
Mar 02, 2012