1DWM

Solution structure of Linum usitatissinum trypsin inhibitor (LUTI)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Determination of a High Precision Structure of a Novel Protein, Linum Usitatissimum Trypsin Inhibitor (Luti), Using Computer-Aided Assignment of Noesy Cross-Peaks

Cierpicki, T.Otlewski, J.

(2000) J.Mol.Biol. 302: 1179

  • DOI: 10.1006/jmbi.2000.4116

  • PubMed Abstract: 
  • The solution structure of a novel 69 residue proteinase inhibitor, Linum usitatissimum trypsin inhibitor (LUTI), was determined using a method based on computer aided assignment of nuclear Overhauser enhancement spectroscopy (NOESY) data. The approac ...

    The solution structure of a novel 69 residue proteinase inhibitor, Linum usitatissimum trypsin inhibitor (LUTI), was determined using a method based on computer aided assignment of nuclear Overhauser enhancement spectroscopy (NOESY) data. The approach applied uses the program NOAH/DYANA for automatic assignment of NOESY cross-peaks. Calculations were carried out using two unassigned NOESY peak lists and a set of determined dihedral angle restraints. In addition, hydrogen bonds involving amide protons were identified during calculations using geometrical criteria and values of HN temperature coefficients. Stereospecific assignment of beta-methylene protons was carried out using a standard procedure based on nuclear Overhauser enhancement intensities and 3J(alpha)(beta) coupling constants. Further stereospecific assignment of methylene protons and diastereotopic methyl groups were established upon structure-based method available in the program GLOMSA and chemical shift calculations. The applied algorithm allowed us to assign 1968 out of 2164 peaks (91%) derived from NOESY spectra recorded in H2O and 2H2O. The final experimental data input consisted of 1609 interproton distance restraints, 88 restraints for 44 hydrogen bonds, 63 torsion angle restraints and 32 stereospecifically assigned methylene proton pairs and methyl groups. The algorithm allowed the calculation of a high precision protein structure without the laborious manual assignment of NOESY cross-peaks. For the 20 best conformers selected out of 40 refined ones in the program CNS, the calculated average pairwise rmsd values for residues 3 to 69 were 0.38 A (backbone atoms) and 1.02 A (all heavy atoms). The three-dimensional LUTI structure consists of a mixed parallel and antiparallel beta-sheet, a single alpha-helix and shows the fold of the potato 1 family of proteinase inhibitors. Compared to known structures of the family, LUTI contains Arg and Trp residues at positions P6' and P8', respectively, instead of two Arg residues, involved in the proteinase binding loop stabilization. A consequence of the ArgTrp substitution at P8' is a slightly more compact conformation of the loop relative to the protein core.


    Organizational Affiliation

    Laboratory of Protein Engineering, Institute of Biochemistry and Molecular Biology, University of Wroclaw, Wroclaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LINUM USITATISSINUM TRYPSIN INHIBITOR
A
70Linum usitatissimumMutation(s): 0 
Find proteins for P82381 (Linum usitatissimum)
Go to UniProtKB:  P82381
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY 
  • Olderado: 1DWM Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance