1N6X | pdb_00001n6x

RIP-phasing on Bovine Trypsin

• PDB DOI: https://doi.org/10.2210/pdb1N6X/pdb

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


• Deposited: 2002-11-12 Released: 2003-03-04 
• Deposition Author(s): Ravelli, R.B.G., Leiros, H.-K.S., Pan, B., Caffrey, M., McSweeney, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.165 (Depositor) 
• R-Value Work: 
  0.138 (Depositor) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures

Ravelli, R.B.G., Leiros, H.-K.S., Pan, B., Caffrey, M., McSweeney, S.

(2003) Structure 11: 217-224

• PubMed: 12575941 
• DOI: https://doi.org/10.1016/s0969-2126(03)00006-6
• Primary Citation Related Structures: 
  1N6X, 1N6Y, 1N7A, 1N7B


• PubMed Abstract: 
  

  The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.

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Organizational Affiliation: 
• European Molecular Biology Laboratory (EMBL) Grenoble Outstation, 6 rue Jules Horowitz, B.P. 181, F38042 9, Grenoble Cedex, France. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.76 kDa 
• Atom Count: 1,953 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsinogen, cationic	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
ABN	E [auth A]	BENZYLAMINE C7 H9 N WGQKYBSKWIADBV-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.165 (Depositor) 
• R-Value Work:  0.138 (Depositor) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.209	α = 90
b = 56.658	β = 90
c = 66.126	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
SCALA	data scaling
SHELXD	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-04 
Deposition Author(s): Ravelli, R.B.G., Leiros, H.-K.S., Pan, B., Caffrey, M., McSweeney, S.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary