› 5ygk

X-ray diffraction
2.05Å resolution

Crystal structure of a synthase from Streptomyces sp. CL190 with dmaspp

Released:
DOI: 10.2210/pdb5ygk/pdb
PDB entry 5ygk coloured by chain, front view.
PDB entry 5ygk coloured by chain, side view.
PDB entry 5ygk coloured by chain, top view.
Source organism: Streptomyces sp. CL190
Primary publication:
Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.
Malwal SR, Gao J, Hu X, Yang Y, Liu W, Huang JW, Ko TP, Li L, Chen CC, O'Dowd B, Khade RL, Zhang Y, Zhang Y, Oldfield E, Guo RT
ACS Catal 8 4299-4312 (2018)
PMID: 30345154

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197873 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclolavandulyl diphosphate synthase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 217 amino acids
Theoretical weight: 24.38 KDa
Source organism: Streptomyces sp. CL190
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: X5IYJ5 (Residues: 1-217; Coverage: 100%)
Sequence domains: Putative undecaprenyl diphosphate synthase

Ligands and Environments

2 bound ligands:
Ligand DST 16 x DST
Ligand MG 8 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P21
Unit cell:
a: 90.09Å b: 119.308Å c: 93.133Å
α: 90° β: 117.35° γ: 90°
R-values:
R R work R free
0.185 0.184 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Isoprenyl diphosphate synthases: the chain length determining step in terpene biosynthesis.
Nagel et al. (2019)
5 other articles

3 mentions without citation

Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases.
Rudolf et al. (2020)
2 more