1HJ9 | pdb_00001hj9

Atomic resolution structures of trypsin provide insight into structural radiation damage

• PDB DOI: https://doi.org/10.2210/pdb1HJ9/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2001-01-10 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: 0.95 Å
• R-Value Free: 
  0.140 (Depositor), 0.115 (DCC) 
• R-Value Work: 
  0.122 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

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: 23.84 kDa 
• Atom Count: 1,965 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-TRYPSIN	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ANL	B [auth A]	ANILINE C6 H7 N PAYRUJLWNCNPSJ-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.140 (Depositor), 0.115 (DCC) 
• R-Value Work:  0.122 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.055	α = 90
b = 56.812	β = 90
c = 66.282	γ = 90

Software Package:

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

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: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2025-04-09
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary
• Version 2.1: 2025-10-01
  Changes: Derived calculations, Structure summary