Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23768.74 
• Atom Count: 1883 
• Residue Count: 223 
• Unique protein chains: 1

4I8L

Bovine trypsin at 0.87 resolution

• DOI: 10.2210/pdb4I8L/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus


• Deposited: 2012-12-03 Released: 2012-12-19 
• Deposition Author(s): Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 0.117 
• R-Value Work: 0.102 

Literature

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.

Liebschner, D., Dauter, M., Brzuszkiewicz, A., Dauter, Z.

(2013) Acta Crystallogr.,Sect.D 69: 1447-1462

• PubMed: 23897468 
• DOI: 10.1107/S0907444913009050
• Primary Citation of Related Structures:  
  4I8K, 4I8J, 4I8H, 4I8G


• PubMed Abstract: 
  

Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(α) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

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Organizational Affiliation: 

Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BEN	A	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 0.117 
• R-Value Work: 0.102 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 54.219	α = 90.00
b = 58.345	β = 90.00
c = 66.239	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	refinement
SHELXL	refinement
SCALEPACK	data scaling
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-03 
• Released Date: 2012-12-19 
• Deposition Author(s): Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A.

Revision History 

• Version 1.0: 2012-12-19
  Type: Initial release
• Version 1.1: 2013-09-18
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description