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 

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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.,Sect.D 51: 725-730

  • DOI: 10.1107/S0907444995000333

  • 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 ha ...

    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: 
    • 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
    • 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.,Sect.B 39: 480
    • 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
    • Crystal Structure Determination and Refinement of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
      Smalas, A.O.,Hordvik, A.
      (1993) Acta Crystallogr.,Sect.D 49: 318
    • 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 --: --
    • The Accuracy of Refined Protein Structures: Comparison of Two Independently Refined Models of Bovine Trypsin
      Chambers, J.H.,Stroud, R.M.
      (1979) Acta Crystallogr.,Sect.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
237Salmo salarMutation(s): 0 
EC: 3.4.21.4
Find proteins for P35031 (Salmo salar)
Go to UniProtKB:  P35031
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.090α = 90.00
b = 82.330β = 90.00
c = 31.160γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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