Structure of IDP90544

Crystal structure of dihydrofolate reductase from Yersinia pestis complexed with methotrexate

Edit deposit information
CSGID target
IDP90544 
PDB Id
4QI9 (NCBI MMDB
Authors
N.Maltseva,Y.Kim,M.Makowska-Grzyska,R.Mulligan,S.Shatsman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
May 30, 2014 
Release Date
Jul 02, 2014 

Annotation

Description
Dihydrofolate reductase is a housekeeping enzyme which is responsible for maintaining the amount of tetrahydrofolate in the cell. It catalyzes the NADPH-linked reduction of 7,8-dihydrofolate to 5,6,7,8- tetrahydrofolate. Tetrahydrofolate is the cofactor used in synthesis of several important metabolites like thymidylate, a building block of DNA. Crystal Structure of Dihydrofolate Reductase from Yersinia pestis complexed with methotrexate was solved at 2.3A resolution. Protein has single domain composed of 4 alpha helices and 8 beta-sheets. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
MTX biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=178.20Å, b=103.64Å, c=34.29Å
α=90.00, β=93.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.24-2.30Å (2.38-2.30Å)  
Rall(%)
19.3 
Rwork(%)
19.1 (21.5) 
Rfree(%)
23.6 (27.6) 
Num. observed reflections
28149 (2240) 
Num. Rfree reflections
1421 (109) 
Completeness(%)
96.6 (82.0) 

Model parameters

Num Atoms
3667  
Num Waters
80  
Num Hetatoms
299  
Model mean isotropic B factor
30.720Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.253°  
RMSD dihedral angle
17.084°
 
Filename uploaded
dep.pdb (uploaded on Jun 26, 2014 12:35 PM)  
Inserted
Jun 26, 2014