1BIT

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

• PDB DOI: https://doi.org/10.2210/pdb1BIT/pdb

• Classification: SERINE PROTEINASE
• Organism(s): Salmo salar
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 15299802 
• DOI: https://doi.org/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 = 61.95, 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.78 kDa 
• Atom Count: 1,811 
• Modelled Residue Count: 222 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN	A	237	Salmo salar	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P35031 (Salmo salar) Explore P35031  Go to UniProtKB:  P35031

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	D [auth A], E [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 77.09	α = 90
b = 82.33	β = 90
c = 31.16	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.5: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary