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Structure of IDP90849

Crystal Structure of Phosphoserine Aminotransferase from Campylobacter jejuni

Edit deposit information
CSGID target
IDP90849 
PDB Id
3M5U (NCBI MMDB
Authors
Y.Kim,M.Gu,L.Papazisi,W.F.Anderson,A.Joachimiak 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 13, 2010 
Release Date
Apr 07, 2010 

Annotation

Description
Phosphoserine aminotransferases is a pyridoxal phosphate dependent enzyme converting O-phospho-L-serine and oxoglutarate to 3-phosphonooxypyruvate and L-glutamate in the major phosphorylated serine biosynthesis pathway. The enzyme is part of the aminotransferase class-V family. The protein structure is a dimer with each subunit consisting of a small and a large domains. The large domain spans residues of 64 – 262 with seven-stranded beta-sheets and four alpha-helices all in one side contacting the same region of the other subunit. The rest of the monomer forms the small domain and between the two domains in a relatively wide open surface, a pyridoxal phosphate binds to a largely positively charged shallow patch. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
GOL
MES 2-(n-morpholino)-ethanesulfonic acid
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=54.74Å, b=105.86Å, c=70.01Å
α=90.00, β=99.22, γ=90.00 
Solvent content
49.17  
Matthews coefficient
2.42  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.86-2.15Å (2.23-2.15Å)  
Rall(%)
17.2 
Rwork(%)
16.9 (22.9) 
Rfree(%)
22.0 (28.3) 
Num. observed reflections
44521 (4092) 
Num. Rfree reflections
2248 (223) 
Completeness(%)
99.2 (96.0) 

Model parameters

Num Atoms
6191  
Num Waters
428  
Num Hetatoms
0  
Model mean isotropic B factor
37.790Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.355°  
RMSD dihedral angle
18.82°
 
Filename uploaded
dep1w.pdb (uploaded on Mar 15, 2010 8:07 AM)  
Inserted
Mar 15, 2010