6SVX

Reference structure of bovine trypsin (odd frames of crystal x33)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.

Gagner, V.A.Lundholm, I.Garcia-Bonete, M.J.Rodilla, H.Friedman, R.Zhaunerchyk, V.Bourenkov, G.Schneider, T.Stake, J.Katona, G.

(2019) Sci Rep 9: 19281-19281

  • DOI: https://doi.org/10.1038/s41598-019-55777-5
  • Primary Citation of Related Structures:  
    6SUX, 6SV0, 6SV6, 6SV8, 6SV9, 6SVB, 6SVD, 6SVG, 6SVI, 6SVJ, 6SVN, 6SVR, 6SVU, 6SVV, 6SVW, 6SVX, 6SVZ, 6SW0

  • PubMed Abstract: 

    Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.37α = 90
b = 56.77β = 90
c = 64.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references