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Structure of IDP00749

Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant.

Edit deposit information
CSGID target
IDP00749 
PDB Id
3PGY (NCBI MMDB
Authors
J.Osipiuk,M.Makowska-Grzyska,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Nov 02, 2010 
Release Date
Nov 17, 2010 

Annotation

Description
Serine hydroxymethyltransferase (SHMT) catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene tetrahydrofolate (5,10-CH2-THF). The reaction requires pyridoxal-phosphate (PLP) as a coenzyme. 5,10-CH2-THF is a key intermediate for the biosynthesis of purines, thymidine, choline and methionine and connects amino acid and nucleotide metabolisms. SHMT also catalyzes THF-independent aldolytic cleavage, decarboxylation, racemization, and transamination reactions. SHMT levels have been found to increase by 5–10-fold in cancer cells. Therefore it is considered as a potential target for the development of anticancer agents. 
Functional assignment
Transferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=69.08Å, b=86.53Å, c=301.81Å
α=90.00, β=90.00, γ=90.00 
Solvent content
50.35  
Matthews coefficient
2.48  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
47.70-1.92Å (1.97-1.92Å)  
Rall(%)
16.8 
Rwork(%)
16.6 (26.2) 
Rfree(%)
20.8 (27.8) 
Num. observed reflections
135637 (9619) 
Num. Rfree reflections
6781 (491) 
Completeness(%)
97.8 (95.1) 

Model parameters

Num Atoms
13941  
Num Waters
1057  
Num Hetatoms
0  
Model mean isotropic B factor
19.010Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.598°  
Filename uploaded
x15_refmac1.pdb (uploaded on Nov 04, 2010 4:38 PM)  
Inserted
Nov 04, 2010