› 6jk5

X-ray diffraction
1.25Å resolution

Ca2+-dependent type II antifreeze protein (Ca2+-free form)

Released:
DOI: 10.2210/pdb6jk5/pdb
PDB entry 6jk5 coloured by chain, front view.
PDB entry 6jk5 coloured by chain, side view.
PDB entry 6jk5 coloured by chain, top view.
Source organism: Hypomesus nipponensis
Primary publication:
Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.
Arai T, Nishimiya Y, Ohyama Y, Kondo H, Tsuda S
OpenAccess logo Biomolecules 9 (2019)
PMID: 31035615

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160884 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C-type lectin domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 136 amino acids
Theoretical weight: 15.32 KDa
Source organism: Hypomesus nipponensis
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P84493 (Residues: 18-147; Coverage: 100%)
Sequence domains: Lectin C-type domain

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P3121
Unit cell:
a: 66.029Å b: 66.029Å c: 50.295Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.18 0.212
Expression system: Komagataella pastoris

Quick links

Citations

2 citation in other articles

Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution.
Ptak-Kaczor et al. (2021)
1 more

2 mentions without citation

Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration.
Tsuda et al. (2020)
1 more