Structure of IDP91519

1.43 Angstrom resolution crystal structure of cell division protein FtsZ (ftsZ) from Staphylococcus epidermidis RP62A in complex with GDP

Edit deposit information
CSGID target
IDP91519 
PDB Id
4M8I (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,J.Winsor,I.Dubrovska,E.V.Filippova,D.B.Olsen,A.Therien,L.Shuvalova,K.Young,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 13, 2013 
Release Date
Sep 04, 2013 

Annotation

Description
The crystal structure of the cell division protein FtsZ (ftsZ; construct with residues 2–392) from Staphylococcus epidermidis RP62A in complex with GDP was determined by molecular replacement and refined to 1.43 A resolution. The PISA and crystal packing analysis did not reveal any assemblies for the single chain of the protein in the C2 asymmetric unit. The tertiary structure of FtsZ consists of two separate domains. An N-terminal domain spans residues 2–222 and consists of a parallel 6-stranded beta-sheet that is flanked by 11 helices. A C-terminal domain is composed of an antiparallel 4-stranded beta-sheet and 2 helices that encompass residues 223–392. The protein is fairly acidic with theoretical pI of 4.8; the C-terminal domain has substantial surface patches of negative charge. Guanosine-5’-diphosphate is bound at a surface exposed pocket in the N-terminal domain. Residues 107–110 and 20–22 create an oxyanion hole that coordinates the diphosphate moiety. The nucleobase portion of the nucleotide is held in place via stacking interactions with Phe183 and hydrogen-bonded contacts with Asn25, Arg29 and Asn166. The sugar moiety interacts with Glu139, Arg143 and Asn166.  
Functional assignment
Cell Cycle 

Ligands

Ligand code Name Ligand type
SO4 crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=71.33Å, b=52.06Å, c=87.00Å
α=90.00, β=109.64, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
27.33-1.43Å (1.47-1.43Å)  
Rall(%)
17.1 
Rwork(%)
16.9 (32.8) 
Rfree(%)
20.6 (41.0) 
Num. observed reflections
53058 (3717) 
Num. Rfree reflections
2705 (187) 
Completeness(%)
95.8 (91.7) 

Model parameters

Num Atoms
2458  
Num Waters
333  
Num Hetatoms
374  
Model mean isotropic B factor
23.410Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.833°  
Filename uploaded
4M8I.pdb (uploaded on Jun 05, 2015 10:55 AM)  
Inserted
Aug 29, 2013