1BIT

THE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN A SECOND CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of anionic salmon trypsin in a second crystal form.

Berglund, G.I.Smalas, A.O.Hordvik, A.Willassen, N.P.

(1995) Acta Crystallogr D Biol Crystallogr 51: 725-730

  • DOI: 10.1107/S0907444995000333
  • Primary Citation of Related Structures:  
    1BIT

  • PubMed Abstract: 
  • Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 A, resolution. The crystals are orthorhombic and belong to space group P2(1)2(1)2 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 A. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61 ...

    Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 A, resolution. The crystals are orthorhombic and belong to space group P2(1)2(1)2 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 A. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b = 84.33 and c = 39.11 A [Smalås & Hordvik (1993). Acta Cryst. D49, 318-330]. The presence of a sulfate group involved in several hydrogen bonds to active-site residues, and the location of an additional benzamidine site in the crystal lattice, are the most striking differences between the present and the previous structure. Superposition of main-chain atoms in the two structures give an overall r.m.s. difference of 0.26 A, with the main differences located to areas with different molecular packing. The overall coordinate error is estimated to be between 0.20 and 0.25 A, by the method of Luzzati.


    Related Citations: 
    • Cold-Adaption of Enzymes: Structural Comparison between Salmon and Bovine Trypsins
      Smalas, A.O., Heimstad, E.S., Hordvik, A., Willassen, N.P.
      () To be published --: --
    • Crystal Structure Determination and Refinement of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
      Smalas, A.O., Hordvik, A.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 318
    • Crystallization and Preliminary X-Ray Crystallographic Studies of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
      Smalas, A.O., Hordvik, A., Hansen, L.K., Hough, E., Jynge, K.
      (1990) J Mol Biol 214: 355
    • Crystal Structure of Bovine B-Trypsin at 1.5 Angstroms Resolution in a Crystal Form with Low Molecular Packing Density
      Bartunik, H.D., Summers, L.J., Bartsch, H.H.
      (1989) J Mol Biol 210: 813
    • The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors
      Marquart, M., Walter, J., Deisenhofer, J., Bode, W., Huber, R.
      (1983) Acta Crystallogr B 39: 480
    • The Accuracy of Refined Protein Structures: Comparison of Two Independently Refined Models of Bovine Trypsin
      Chambers, J.H., Stroud, R.M.
      (1979) Acta Crystallogr B 35: 1861

    Organizational Affiliation

    Protein Crystallography Group, Department of Chemistry, Institute of Mathematical and Physical Sciences, University of Tromsø, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSINA237Salmo salarMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P35031 (Salmo salar)
Explore P35031 
Go to UniProtKB:  P35031
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.09α = 90
b = 82.33β = 90
c = 31.16γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1994-08-26 
  • Released Date: 1994-11-01 
  • Deposition Author(s): Berglund, G.I.

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Advisory, Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description