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Structure of IDP04560

Crystal Structure of Phosphoribosylaminoimidazole-Succinocarboxamide Synthase from Clostridium perfringens

Edit deposit information
CSGID target
IDP04560 
PDB Id
3NUA (NCBI MMDB
Authors
Y.Kim,R.Mulligan,K.Kwon,W.F.Anderson,A.Joachimiak 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 06, 2010 
Release Date
Aug 25, 2010 

Annotation

Description
Also known as SAICAR synthetase, phosphoribosylaminoimidazole-succinocarboxamide synthase catalyzes the seventh step in the de novo purine biosynthetic pathway; the ATP-dependent conversion of 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid and aspartic acid to SAICAR. Overall the 1.4 A structure is similar to other reported structures of an alpha-beta fold with two anti-parallel beta-sheets surrounded by seven alpha helices. The structure is a symmetric dimer formed by the interaction between the small alpha-helices and the edges of the beta-sheet in the middle domain. An ADP and an AMP molecules processed from ATP added during the crystallization were found in the groove formed between the two beta-sheets in each monomer. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
ADP
AMP
GOL
CIT

Structure information

Unit cell parameters

Space Group
P 21 21 2  
Unit Cell

a=80.88Å, b=148.91Å, c=45.31Å
α=90.00, β=90.00, γ=90.00 
Solvent content
50.76  
Matthews coefficient
2.5  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
38.21-1.40Å (1.45-1.40Å)  
Rall(%)
14.4 
Rwork(%)
14.3 (19.8) 
Rfree(%)
16.1 (21.8) 
Num. observed reflections
113879 (10703) 
Num. Rfree reflections
5705 (522) 
Completeness(%)
99.9 (100.0) 

Model parameters

Num Atoms
4948  
Num Waters
711  
Num Hetatoms
82  
Model mean isotropic B factor
19.700Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.500°  
RMSD dihedral angle
18.288°
 
Filename uploaded
rcsb060288-rev.pdb (uploaded on Jul 14, 2010 8:01 AM)  
Inserted
Jul 06, 2010