› 3b6n

X-ray diffraction
2.26Å resolution

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax

Released:
DOI: 10.2210/pdb3b6n/pdb
PDB entry 3b6n coloured by chain, front view.
PDB entry 3b6n coloured by chain, side view.
PDB entry 3b6n coloured by chain, top view.
Source organism: Plasmodium vivax Sal-1
Entry authors: Wernimont AK, Lew J, Kozieradzki I, Lin YH, Sun X, Khuu C, Zhao Y, Schapira M, Arrowsmith CH, Edwards AM, Weigelt J, Bochkarev A, Hui R, Artz JD, Xiao T, Structural Genomics Consortium (SGC)

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-107701 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 187 amino acids
Theoretical weight: 20.22 KDa
Source organism: Plasmodium vivax Sal-1
Expression system: Escherichia coli
UniProt:
  • Canonical: A5KBP6 (Residues: 102-287; Coverage: 65%)
Gene name: PVX_003920
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ DW
Spacegroup: P213
Unit cell:
a: 79.661Å b: 79.661Å c: 79.661Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.204 0.257
Expression system: Escherichia coli

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