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Structure of IDP02550

Crystal Structure of Exopolyphosphatase from Yersinia pestis

Edit deposit information
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

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 crystallization
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=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