1HJ8 | pdb_00001hj8

1.00 AA Trypsin from Atlantic Salmon

• PDB DOI: https://doi.org/10.2210/pdb1HJ8/pdb

• Classification: HYDROLASE
• Organism(s): Salmo salar
• Mutation(s): No 


• Deposited: 2001-01-09 Released: 2002-01-04 
• Deposition Author(s): Leiros, H.-K.S., Mcsweeney, S.M., Smalas, A.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.149 (Depositor), 0.121 (DCC) 
• R-Value Work: 
  0.120 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Starting Model: experimental

Literature

Atomic Resolution Structure of Trypsin Provide Insight Into Structural Radiation Damage

Leiros, H.-K.S., Mcsweeney, S.M., Smalas, A.O.

(2001) Acta Crystallogr D Biol Crystallogr 57: 488

• PubMed: 11264577 
• DOI: https://doi.org/10.1107/s0907444901000646
• Primary Citation Related Structures: 
  1HJ8, 1HJ9


• PubMed Abstract: 
  

  Radiation damage is an inherent problem in protein X-ray crystallography and the process has recently been shown to be highly specific, exhibiting features such as cleavage of disulfide bonds, decarboxylation of acidic residues, increase in atomic B factors and increase in unit-cell volume. Reported here are two trypsin structures at atomic resolution (1.00 and 0.95 A), the data for which were collected at a third-generation synchrotron (ESRF) at two different beamlines. Both trypsin structures exhibit broken disulfide bonds; in particular, the bond from Cys191 to Cys220 is very sensitive to synchrotron radiation. The data set collected at the most intense beamline (ID14-EH4) shows increased structural radiation damage in terms of lower occupancies for cysteine residues, more breakage in the six disulfide bonds and more alternate conformations. It appears that high intensity and not only the total X-ray dose is most harmful to protein crystals.

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Organizational Affiliation: 
• Protein Crystallography Group, Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 24.21 kDa 
• Atom Count: 2,062 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN I	A	222	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	B [auth A], C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.149 (Depositor), 0.121 (DCC) 
• R-Value Work:  0.120 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.63	α = 90
b = 82.77	β = 90
c = 30.92	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-04 
Deposition Author(s): Leiros, H.-K.S., Mcsweeney, S.M., Smalas, A.O.

Revision History  

• Version 1.0: 2002-01-04
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Data collection, Derived calculations, Other, Refinement description, Version format compliance
• Version 2.0: 2021-08-04
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.2: 2025-10-01
  Changes: Derived calculations, Structure summary