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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 ADENOSINE MONOPHOSPHATE
GOL glycerol
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