3CI2

REFINEMENT OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF BARLEY SERINE PROTEINASE INHIBITOR 2 AND COMPARISON WITH THE STRUCTURES IN CRYSTALS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals.

Ludvigsen, S.Shen, H.Y.Kjaer, M.Madsen, J.C.Poulsen, F.M.

(1991) J.Mol.Biol. 222: 621-635


  • PubMed Abstract: 
  • The three-dimensional structure of barley serine proteinase inhibitor, CI-2, has been determined using nuclear magnetic resonance spectroscopy. The present structure determination is a refinement of the structure previously determined by us, using in ...

    The three-dimensional structure of barley serine proteinase inhibitor, CI-2, has been determined using nuclear magnetic resonance spectroscopy. The present structure determination is a refinement of the structure previously determined by us, using in the present case stereo-specific assignments, and a virtually complete set of assignments of the two-dimensional nuclear Overhauser spectrum. The structure determination is based on the identification of more than 1300 nuclear Overhauser effects, of which 961 were used in the structure calculation as distance restraints, and on 94 dihedral angle restraints, of which 31 are for chi 1 angles in defined chiral centers. These have been used to calculate a series of 20 three-dimensional structures using a combination of distance geometry, simulated annealing and restrained molecular dynamics. Each of the 20 structures was in agreement within less than 0.5 A of each of the distance restraints and with all dihedral angle restraints. When compared to the geometric average structure of the 20 refined structures the root-mean-square differences for the backbone atoms were 0.8 (+/- 0.2) A and for all atoms were 1.6 (+/- 0.2) A. By comparison, the values obtained for the structures determined previously were 1.4 (+/- 0.2) A and 2.1 (+/- 0.1) A, respectively. The structures were also compared to the structure determined in the crystalline state by X-ray diffraction showing root-mean-square differences of 1.6 (+/- 0.2) A and 2.8 (+/- 0.2) A for the backbone and all atoms, respectively. Common features of the solution structure and the two crystal structures are the four-stranded beta-structure, composed of a pair of parallel strands, and three pairs of antiparallel beta-strands flanked on one side by a 12-residue alpha-helix and on the other side by a loop containing the serine proteinase binding site. The new analysis of the structure has revealed an additional pair of antiparallel beta-strands, consisting of residues 65 to 67 and 81 to 83, that was not seen in either of the crystal structures or the previous solution structure. Identification of this was based on nuclear magnetic resonance evidence for the hydrogen bond (67HN to 81CO) not reported previously. Also the presence of a bifurcated hydrogen bond involving Phe69 CO and HN atoms of Ala77 and Gln78 was observed in solution but not in crystals. Minor differences between the two structures were observed in the phi-angles of residues Met59 and Glu60 in the inhibitory site.


    Related Citations: 
    • Accurate Measurements of Coupling Constants from Two-Dimensional Nuclear Magnetic Resonance Spectra of Proteins and Determination of Phi-Angles
      Ludvigsen, S.,Andersen, K.V.,Poulsen, F.M.
      (1991) J.Mol.Biol. 217: 731
    • Comparison of the Solution and X-Ray Structures of Barley Serine Proteinase Inhibitor 2
      Clore, G.M.,Gronenborn, A.M.,James, M.N.G.,Kjaer, M.,Mcphalen, C.A.,Poulsen, F.M.
      (1987) Protein Eng. 1: 313
    • Secondary Structure of Barley Serine Proteinase Inhibitor 2 Determined by Proton Nuclear Magnetic Resonance Spectroscopy
      Kjaer, M.,Poulsen, F.M.
      (1987) Carlsberg Res.Commun. 52: 355
    • The Determination of the Three-Dimensional Structure of Barley Serine Proteinase Inhibitor 2 by Nuclear Magnetic Resonance, Distance Geometry and Restrained Molecular Dynamics
      Clore, G.M.,Gronenborn, A.M.,Kjaer, M.,Poulsen, F.M.
      (1987) Protein Eng. 1: 305
    • Sequence Specific Assignment of the Proton Nuclear Magnetic Resonance Spectrum of Barley Serine Proteinase Inhibitor 2
      Kjaer, M.,Ludvigsen, S.,Sorensen, O.W.,Denys, L.A.,Kindtler, J.,Poulsen, F.M.
      (1987) Carlsberg Res.Commun. 52: 327
    • The Three-Dimensional Structure of Barley Serine Proteinase Inhibitor-2 in Solution as Determined by Proton Nuclear Magnetic Resonance Spectroscopy
      Poulsen, F.M.,Kjaer, M.,Clore, G.M.,Gronenborn, A.M.
      (1988) Alfred Benzon Symp. 26: 234
    • Application of Symmetry Projection Operators to Measurements of Coupling Constants in 2D NMR Spectra of Proteins
      Shen, H.,Ludvigsen, S.,Poulsen, F.M.
      (1990) J.Magn.Reson. 90: 346


    Organizational Affiliation

    Kemisk Afdeling, Carlsberg Laboratorium, Valby Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHYMOTRYPSIN INHIBITOR 2
A
66Hordeum vulgareMutation(s): 0 
Find proteins for P01053 (Hordeum vulgare)
Go to UniProtKB:  P01053
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1991-09-10 
  • Released Date: 1993-10-31 
  • Deposition Author(s): Poulsen, F.M.

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other