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Structure of IDP90905

Phosphoribosylformylglycinamidine cyclo-ligase from Vibrio cholerae.

Edit deposit information
CSGID target
IDP90905 
PDB Id
3P4E (NCBI MMDB
Authors
J.Osipiuk,M.Zhou,L.Papazisi,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Oct 06, 2010 
Release Date
Oct 20, 2010 

Annotation

Description
Phosphoribosylformylglycinamidine cyclo-ligase (also called phosphoribosylaminoimidazole synthetase, aminoimidazole ribonucleotide synthetase and PurM protein) catalyzes the conversion of ATP and N-formylglycinamide ribonucleotide (FGAM) to aminoimidazole ribonucleotide (AIR), ADP, and phosphate. This reaction is the fifth step in purine biosynthesis. An O-phosphorylated amide intermediate is created in the reaction, which after attack by the N1 of the amidine of FGAM forms a five-membered ring that can lose both phosphate and a proton to generate AIR. A similar mechanism also occurs for FGAM synthetase (PurL protein) in the fourth step of purine biosynthesis. 
Functional assignment
Ligase 

Ligands

Ligand code Name Ligand type
CIT crystallization
EDO crystallization
GOL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 32 2 1  
Unit Cell

a=106.28Å, b=106.28Å, c=61.38Å
α=90.00, β=90.00, γ=120.00 
Solvent content
54.42  
Matthews coefficient
2.7  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
40.17-1.77Å (1.82-1.77Å)  
Rall(%)
15.0 
Rwork(%)
14.9 (28.1) 
Rfree(%)
17.5 (31.0) 
Num. observed reflections
39087 (2828) 
Num. Rfree reflections
1954 (150) 
Completeness(%)
99.7 (98.8) 

Model parameters

Num Atoms
2908  
Num Waters
282  
Num Hetatoms
0  
Model mean isotropic B factor
17.680Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.703°  
Filename uploaded
y81d_refmac1.pdb (uploaded on Oct 07, 2010 2:43 PM)  
Inserted
Oct 07, 2010