› 3fpi

X-ray diffraction
2.8Å resolution

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

Released:
DOI: 10.2210/pdb3fpi/pdb
PDB entry 3fpi coloured by chain, front view.
PDB entry 3fpi coloured by chain, side view.
PDB entry 3fpi coloured by chain, top view.
Source organism: Yersinia pestis CO92
Entry authors: Kim Y, Maltseva N, Stam J, Anderson WF, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

Reaction catalysed: 
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187190 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 17.66 KDa
Source organism: Yersinia pestis CO92
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZBP7 (Residues: 1-162; Coverage: 100%)
Gene names: YPO3360, YP_0327, ispF, y0829
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

5 bound ligands:
Ligand CTP 1 x CTP
Ligand EPE 1 x EPE
Ligand CL 1 x CL
Ligand SO4 1 x SO4
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: I213
Unit cell:
a: 145.639Å b: 145.639Å c: 145.639Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.199
Expression system: Escherichia coli

Quick links