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Structure of IDP02274

1.95 Angstrom Resolution Crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate Phosphatase from Yersinia pestis.

Edit deposit information
CSGID target
IDP02274 
PDB Id
3IJ5 (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Aug 03, 2009 
Release Date
Aug 11, 2009 

Annotation

Description
3-Deoxy-D-manno-octulosonate (KDO) is a carbohydrate molecule required for integrity of Gram-negative bacterial outer membrane, therefore its biosynthesis is a potential antibiotic target. In addition to serving as a linker molecule in the lipopolysaccharide layer on the outer membrane, KDO is also found as a building block of the capsular polysaccharide. Four enzymes encoded by the kds genes are required for the biosynthesis of the activated form of KDO. The third enzyme, 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) phosphatase (KdsC), catalyzes the hydrolysis of KDO8P to form KDO and inorganic phosphate. Subsequently, KDO is activated to cytidine monophosphate-KDO by the cytidylyltransferase (KdsB). KDO8P synthase is a homotetramer with the eight strand intramolecular beta barrel. Presented crystal structure of the KdsC from Yersinia pestis is homolog (about 75% homology) of the YrbI from Escherichia coli. To gain mechanistic insights in order to design inhibitors, more structures of the proteins and their complexes from different organisms are necessary. 
Functional assignment
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=130.60Å, b=77.94Å, c=96.88Å
α=90.00, β=120.05, γ=90.00 
Solvent content
46.83  
Matthews coefficient
2.31  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.91-1.95Å (2.00-1.95Å)  
Rall(%)
16.5 
Rwork(%)
16.3 (18.5) 
Rfree(%)
20.2 (27.8) 
Num. observed reflections
60363 (4322) 
Num. Rfree reflections
3078 (213) 
Completeness(%)
98.4 (96.4) 

Model parameters

Num Atoms
5811  
Num Waters
653  
Num Hetatoms
683  
Model mean isotropic B factor
20.080Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.331°  
Filename uploaded
rcsb054476.pdb (uploaded on Aug 05, 2009 5:11 PM)  
Inserted
Aug 05, 2009