6JK5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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.

(2019) Biomolecules 9

  • DOI: 10.3390/biom9050162
  • Primary Citation of Related Structures:  
    6JK4, 6JK5

  • PubMed Abstract: 
  • Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca 2+ -dependent species of AFP, however, it has not been clarified how 1 mol of Ca 2+ -binding is related with the hydration and the ice-binding ability ...

    Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca 2+ -dependent species of AFP, however, it has not been clarified how 1 mol of Ca 2+ -binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca 2+ -dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis , in both Ca 2+ -bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca 2+ -binding site. Firstly, the side-chains of four of the five Ca 2+ -binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca 2+ -bound state. Second, a Ca 2+ -binding loop consisting of a segment D94-E99 becomes less flexible by the Ca 2+ -binding. Third, the Ca 2+ -binding induces a generation of ice-like clathrate waters around the Ca 2+ -binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca 2+ -binding enables the ice-binding of this protein.


    Organizational Affiliation

    OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8563, Japan. s.tsuda@aist.go.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type II antifreeze proteinA136Hypomesus nipponensisMutation(s): 1 
UniProt
Find proteins for P84493 (Hypomesus nipponensis)
Explore P84493 
Go to UniProtKB:  P84493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84493
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.029α = 90
b = 66.029β = 90
c = 50.295γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release