Structure of IDP90846

Crystal structure of GTP cyclohydrolase I from Yersinia pestis CO92 complexed with GTP

Edit deposit information
CSGID target
IDP90846 
PDB Id
4DU6 (NCBI MMDB
Authors
N.Maltseva,Y.Kim,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Feb 21, 2012 
Release Date
Mar 21, 2012 

Annotation

Description
GTP cyclohydrolase I (encoded by gene folE) is the first Zn(2+)-dependent enzyme of the de novo tetrahydrofolate biosynthetic pathway. It presents in bacteria, fungi, and plants. It catalyzes the conversion of GTP to 7,8-dihydroneopterin triphosphate. The 2.1A resolution structure of GTP cyclohydrolase I from Yersinia pestis CO92 is a pentomer in the asymmetric unit. The structure contains, in the active site, five GTP molecules and Ca(2+) ions probably from crystallization in place of Zn(2+) determined by atomic distances and fluorescence spectrum. 
Functional assignment
hydrolase 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological
GOL crystallization
CA crystallization
TRS Tris(hydroxymethyl)aminomethane crystallization
PEG crystallization

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=174.05Å, b=104.91Å, c=70.07Å
α=90.00, β=96.89, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
43.20-2.11Å (2.13-2.11Å)  
Rall(%)
18.2 
Rwork(%)
18.0 (28.0) 
Rfree(%)
22.5 (34.0) 
Num. observed reflections
73168 (2097) 
Num. Rfree reflections
3694 (93) 
Completeness(%)
96.3 (72.0) 

Model parameters

Num Atoms
8818  
Num Waters
182  
Num Hetatoms
345  
Model mean isotropic B factor
57.050Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.482°  
RMSD dihedral angle
18°
 
Filename uploaded
dep.pdb (uploaded on Feb 22, 2012 3:00 PM)  
Inserted
Feb 22, 2012