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Structure of IDP02712

1.55 Angstrom Resolution Crystal Structure of Peptidase T (pepT-1) from Bacillus anthracis str. 'Ames Ancestor'.

Edit deposit information
CSGID target
IDP02712 
PDB Id
3IFE (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jul 24, 2009 
Release Date
Aug 04, 2009 

Annotation

Description
Peptidase T is an aminopeptidase, which hydrolyzes tripeptides containing N-terminal methionine, leucine, or phenylalanine. The protein comprises of two domains: a catalytic domain with an active site containing two metal ions (Zn2+), and a smaller domain, which is involved in a dimer formation. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Around half of the known metalloproteases contain an HEXXH motif, which forms part of the metal-binding site. Comparison of the active sites of peptidase T, carboxypeptidase G2, Aeromonas proteolytica aminopeptidase, carboxypeptidase A and leucine aminopeptidase reveals a common structural framework with interesting similarities and differences in the active sites and in the zinc coordination. 
Functional assignment
Peptidase T, tripeptidase 

Ligands

Ligand code Name Ligand type
ZN
NA Sodium ion
SO4
SUC

Structure information

Unit cell parameters

Space Group
P 21 21 2  
Unit Cell

a=89.22Å, b=142.74Å, c=40.99Å
α=90.00, β=90.00, γ=90.00 
Solvent content
54.1  
Matthews coefficient
2.68  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.11-1.55Å (1.59-1.55Å)  
Rall(%)
15.0 
Rwork(%)
14.8 (20.0) 
Rfree(%)
17.2 (21.5) 
Num. observed reflections
76973 (5626) 
Num. Rfree reflections
3848 (265) 
Completeness(%)
99.9 (99.6) 

Model parameters

Num Atoms
3593  
Num Waters
586  
Num Hetatoms
669  
Model mean isotropic B factor
12.400Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.493°  
Filename uploaded
rcsb054342.pdb (uploaded on Jul 29, 2009 11:52 AM)  
Inserted
Jul 29, 2009