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Structure of IDP02550

Crystal Structure of Exopolyphosphatase from Yersinia pestis

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CSGID target
IDP02550 
PDB Id
3RF0 (NCBI MMDB) 
Authors
Y.Kim,M.Zhou,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Apr 05, 2011 
Release Date
Apr 27, 2011 

Annotation

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Description
This enzyme is involved in purine metabolism catalyzing the reaction to remove one phosphate from a polyphosphate. The enzyme structure from Yersinia pestis CO92 contains only 209 C-terminal residues corresponding the domain III and IV of a full-lenth Ppx, in which domain III of six alpha-helices is similar to that of the N-terminal, HD domain of SpoT and domain IV of an alpha-helix and a three-stranded beta sheet resembles to a part of heat-shock transcription factor.  
Functional assignment
 

Ligands

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

Structure information

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Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=60.41Å, b=71.08Å, c=60.20Å
α=90.00, β=118.29, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.19-1.80Å (1.84-1.80Å)  
Rall(%)
17.9 
Rwork(%)
17.7 (26.5) 
Rfree(%)
22.8 (32.3) 
Num. observed reflections
42408 (2639) 
Num. Rfree reflections
2137 (141) 
Completeness(%)
97.0 (96.0) 

Model parameters

Num Atoms
3632  
Num Waters
466  
Num Hetatoms
469  
Model mean isotropic B factor
28.580Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.366°  
RMSD dihedral angle
15°
 
Filename uploaded
dep.pdb (uploaded on Apr 05, 2011 1:18 PM)  
Inserted
Apr 05, 2011