› 2bd1

X-ray diffraction
1.9Å resolution

A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2

Released:
DOI: 10.2210/pdb2bd1/pdb
PDB entry 2bd1 coloured by chain, front view.
PDB entry 2bd1 coloured by chain, side view.
PDB entry 2bd1 coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A2.
Sekar K, Yogavel M, Kanaujia SP, Sharma A, Velmurugan D, Poi MJ, Dauter Z, Tsai MD
Acta Crystallogr D Biol Crystallogr 62 717-24 (2006)
PMID: 16790927

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132750 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phospholipase A2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 123 amino acids
Theoretical weight: 13.82 KDa
Source organism: Bos taurus
Expression system: Escherichia coli
UniProt:
  • Canonical: P00593 (Residues: 23-145; Coverage: 95%)
Gene name: PLA2G1B
Sequence domains: Phospholipase A2
Structure domains: Phospholipase A2 domain

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand MPD 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MACSCIENCE
Spacegroup: C2
Unit cell:
a: 74.58Å b: 48.69Å c: 67.55Å
α: 90° β: 102.3° γ: 90°
R-values:
R R work R free
0.207 0.207 0.24
Expression system: Escherichia coli

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Citations

1 citations in other articles

Unraveling the structural and chemical features of biological short hydrogen bonds.
Zhou et al. (2019)

1 mention without citation

Surprises and pitfalls arising from (pseudo)symmetry.
Zwart et al. (2008)