1DPO

STRUCTURE OF RAT TRYPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures.

Earnest, T.Fauman, E.Craik, C.S.Stroud, R.

(1991) Proteins 10: 171-187

  • DOI: 10.1002/prot.340100303

  • PubMed Abstract: 
  • The structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 A and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dim ...

    The structure of a rat trypsin mutant [S195C] at a temperature of 120 K has been refined to a crystallographic R factor of 17.4% between 12.0 and 1.59 A and is compared with the structure of the D102N mutant at 295 K. A reduction in the unit cell dimensions in going from room temperature to low temperature is accompanied by a decrease in molecular surface area and radius of gyration. The overall structure remains similar to that at room temperature. The attainable resolution appears to be improved due to the decrease in the fall off of intensities with resolution [reduction of the temperature factor]. This decreases the uncertainty in the atomic positions and allows the localization of more protein atoms and solvent molecules in the low temperature map. The largest differences between the two models occur at residues with higher than average temperature factors. Several features can be localized in the solvent region of the 120 K map that are not seen in the 295 K map. These include several more water molecules as well as an interstitial sulfate ion and two interstitial benzamidine molecules.


    Related Citations: 
    • The Three-Dimensional Structure of Asn102 Mutant of Trypsin: Role of Asp102 in Serine Protease Catalysis
      Sprang, S.,Standing, T.,Fletterick, R.J.,Stroud, R.M.,Finer-Moore, J.,Xuong, N.H.,Hamlin, R.,Rutter, W.J.,Craik, C.S.
      (1987) Science 237: 905


    Organizational Affiliation

    Department of Biochemistry, University of California School of Medicine, San Francisco 94143-0448.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Rattus norvegicusGene Names: Prss2 (Try2)
EC: 3.4.21.4
Find proteins for P00763 (Rattus norvegicus)
Go to UniProtKB:  P00763
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Work: 0.174 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 123.120α = 90.00
b = 123.120β = 90.00
c = 123.120γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata collection
PROLSQrefinement
XENGENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-03-31 
  • Released Date: 1997-07-07 
  • Deposition Author(s): Stroud, R.M.

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance