1GDU

FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 

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This is version 1.4 of the entry. See complete history. 


Literature

Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.

Rypniewski, W.R., Ostergaard, P.R., Norregaard-Madsen, M., Dauter, M., Wilson, K.S.

(2001) Acta Crystallogr D Biol Crystallogr 57: 8-19

  • DOI: 10.1107/s0907444900014116
  • Primary Citation of Related Structures:  
    1FN8, 1GDU, 1GDQ, 1GDN, 1FY5, 1FY4

  • PubMed Abstract: 

    • The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.0 ...

    The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site.

    Related Citations: 
    • Structure of inhibited trypsin from Fusarium oxysporum at 1.55A
      Rypniewski, W.R., Dambmann, C., von der Osten, C., Dauter, M., Wilson, K.S.
      () To be published --: --
    Organizational Affiliation: 

    European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. wojtek@embl-hamburg.de



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPSIN A224Fusarium oxysporumMutation(s): 0 
EC: 3.4.21.4
Find proteins for P35049 (Fusarium oxysporum)
Explore P35049 
Go to UniProtKB:  P35049
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-ALA-ARG B3N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.29α = 102.46
b = 37.05β = 103.81
c = 40.259γ = 102.07
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2018-04-04
    Changes: Data collection