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Structure of IDP00971

Crystal Structure of Short Chain Dehydrogenase (YCIK) from Salmonella enterica subsp. Enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.

Edit deposit information
CSGID target
IDP00971 
PDB Id
3IAH (NCBI MMDB
Authors
G.Minasov,A.Halavaty,T.Skarina,O.Onopriyenko,S.N.Peterson,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jul 14, 2009 
Release Date
Jul 21, 2009 

Annotation

Description
The short-chain dehydrogenases/reductases (SDR) are members of a very large family of enzymes, most of which are known to be NAD- or NADP-dependent oxidoreductases. Drosophila alcohol dehydrogenase was the first member of this family to be characterized. This family used to be called 'insect-type', or 'short-chain' alcohol dehydrogenases. Most dehydrogenases possess at least 2 domains, the first binding the coenzyme, often NAD, and the second binding the substrate. This latter domain determines the substrate specificity and contains amino acids involved in catalysis. Little sequence similarity has been found in the coenzyme binding domain although there is a large degree of structural similarity, and it has therefore been suggested that the structure of dehydrogenases has arisen through gene fusion of a common ancestral coenzyme nucleotide sequence with various substrate specific domains.  
Functional assignment
dehydrogenase/reductase 

Ligands

Ligand code Name Ligand type
CL crystallization
EOH ethanol crystallization
MSE modified residue
NAP biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=158.66Å, b=43.30Å, c=71.92Å
α=90.00, β=93.24, γ=90.00 
Solvent content
42.46  
Matthews coefficient
2.14  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.43-1.83Å (1.88-1.83Å)  
Rall(%)
14.5 
Rwork(%)
14.3 (20.4) 
Rfree(%)
17.6 (24.4) 
Num. observed reflections
43395 (3165) 
Num. Rfree reflections
2169 (152) 
Completeness(%)
99.9 (99.9) 

Model parameters

Num Atoms
3915  
Num Waters
476  
Num Hetatoms
774  
Model mean isotropic B factor
14.130Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.581°  
Filename uploaded
rcsb054168.pdb (uploaded on Jul 24, 2009 5:07 PM)  
Inserted
Jul 24, 2009