7ZVY

Thermococcus kadokarensis phosphomannose isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Unravelling the Adaptation Mechanisms to High Pressure in Proteins.

Calio, A.Dubois, C.Fontanay, S.Koza, M.M.Hoh, F.Roumestand, C.Oger, P.Peters, J.

(2022) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms23158469
  • Primary Citation of Related Structures:  
    7ZVM, 7ZVY

  • PubMed Abstract: 

    Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein-water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.


  • Organizational Affiliation

    Université de Lyon, UCBL, INSA Lyon, CNRS, MAP UMR 5240, 69621 Villeurbanne, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin_2 domain-containing protein
A, C, D, F
116Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0503
UniProt
Find proteins for Q5JD98 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JD98 
Go to UniProtKB:  Q5JD98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JD98
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin_2 domain-containing protein114Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0503
UniProt
Find proteins for Q5JD98 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JD98 
Go to UniProtKB:  Q5JD98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JD98
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin_2 domain-containing protein
E, H
110Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0503
UniProt
Find proteins for Q5JD98 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JD98 
Go to UniProtKB:  Q5JD98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JD98
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin_2 domain-containing protein105Thermococcus kodakarensisMutation(s): 0 
Gene Names: TK0503
UniProt
Find proteins for Q5JD98 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JD98 
Go to UniProtKB:  Q5JD98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JD98
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.158α = 90
b = 91.158β = 90
c = 113.378γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release