› 3rlg

X-ray diffraction
1.6Å resolution

Crystal structure of Loxosceles intermedia phospholipase D isoform 1 H12A mutant

Released:
DOI: 10.2210/pdb3rlg/pdb
PDB entry 3rlg coloured by chain, front view.
PDB entry 3rlg coloured by chain, side view.
PDB entry 3rlg coloured by chain, top view.
Source organism: Loxosceles intermedia
Primary publication:
Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom.
Ullah A, de Giuseppe PO, Murakami MT, Trevisan-Silva D, Wille AC, Chaves-Moreira D, Gremski LH, da Silveira RB, Sennf-Ribeiro A, Chaim OM, Veiga SS, Arni RK
Acta Crystallogr Sect F Struct Biol Cryst Commun 67 234-6 (2011)
PMID: 21301094

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143221 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dermonecrotic toxin LiSicTox-alphaIA1a Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 33.67 KDa
Source organism: Loxosceles intermedia
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CE80 (Residues: 28-306; Coverage: 97%)
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand EDO 4 x EDO
Ligand PEG 2 x PEG
Ligand PGE 2 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: P21
Unit cell:
a: 49.575Å b: 49.455Å c: 56.395Å
α: 90° β: 105.56° γ: 90°
R-values:
R R work R free
0.166 0.164 0.198
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Recent advances in the understanding of brown spider venoms: From the biology of spiders to the molecular mechanisms of toxins.
Gremski et al. (2014)
1 more

3 mentions without citation

Brown Spider (Loxosceles) Venom Toxins as Potential Biotools for the Development of Novel Therapeutics.
Chaves-Moreira et al. (2019)
2 more