2OVO

THE CRYSTAL AND MOLECULAR STRUCTURE OF THE THIRD DOMAIN OF SILVER PHEASANT OVOMUCOID (OMSVP3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3).

Bode, W.Epp, O.Huber, R.Laskowski Jr., M.Ardelt, W.

(1985) Eur.J.Biochem. 147: 387-395


  • PubMed Abstract: 
  • OMSVP3 and OMTKY3 (third domains of silver pheasant and turkey ovomucoid inhibitor) are Kazal-type serine proteinase inhibitors. They have been isomorphously crystallized in the monoclinic space group C2 with cell dimensions of a = 4.429 nm, b = 2.11 ...

    OMSVP3 and OMTKY3 (third domains of silver pheasant and turkey ovomucoid inhibitor) are Kazal-type serine proteinase inhibitors. They have been isomorphously crystallized in the monoclinic space group C2 with cell dimensions of a = 4.429 nm, b = 2.115 nm, c = 4.405 nm, beta = 107 degrees. The asymmetric unit contains one molecule corresponding to an extremely low volume per unit molecular mass of 0.0017 nm3/Da. Data collection was only possible for the OMSVP3 crystals. Orientation and position of the OMSVP3 molecules in the monoclinic unit cells were determined using Patterson search methods and the known structure of the third domain of Japanese quail ovomucoid (OMJPQ3) [Papamokos, E., Weber, E., Bode, W., Huber, R., Empie, M. W., Kato, I. and Laskowski, M., Jr (1982) J. Mol. Biol. 158, 515-537]. The OMSVP3 structure has been refined by restrained crystallographic refinement yielding a final R value of 0.199 for data to 0.15 nm resolution. Conformation and hydrogen-bonding pattern of OMSVP3 and OMJPQ3 are very similar. Large deviations occur at the NH2 terminus owing to different crystal packing, and at the C terminus of the central helix, representing an intrinsic property and resulting from amino acid substitutions far away from this site. The deviation of OMSVP3 from OMTKY3 complexed with the Streptomyces griseus protease B is very small [Fujinaga, M., Read, R. J., Sielecki, A., Ardelt, W., Laskowski, M., Jr and James, M. N. G. (1982) Proc. Natl Acad. Sci. USA, 79, 4868-4872].


    Related Citations: 
    • Thermodynamics and Kinetics of Single Residue Replacements in Avian Ovomucoid Third Domains. Effect on Inhibitor Interactions with Serine Proteinases
      Empie, M.W.,Laskowskijunior, M.
      (1982) Biochemistry 21: 2274
    • Crystallization, Crystal Structure Analysis and Molecular Model of the Third Domain of Japanese Quail Ovomucoid, a Kazal Type Inhibitor
      Weber, E.,Papamokos, E.,Bode, W.,Huber, R.,Kato, I.,Laskowskijunior, M.
      (1981) J.Mol.Biol. 149: 109
    • Structure of the Complex of Streptomyces Griseus Protease B and the Third Domain of the Turkey Ovomucoid Inhibitor at 1.8-Angstroms Resolution
      Read, R.J.,Fujinaga, M.,Sielecki, A.R.,James, M.N.G.
      (1983) Biochemistry 22: 4420
    • Correlation of Amino Acid Sequence with Inhibitor Activity and Specificity of Protein Inhibitors of Serine Proteinases
      Laskowskijunior, M.,Empie, M.W.,Kato, I.,Kohr, W.J.,Ardelt, W.,Bogardjunior, W.C.,Weber, E.,Papamokos, E.,Bode, W.,Huber, R.
      (1981) Colloq.Ges.Biol.Chem. 32: 136
    • Crystallographic Refinement of Japanese Quail Ovomucoid, a Kazal-Type Inhibitor, and Model Building Studies of Complexes with Serine Proteases
      Papamokos, E.,Weber, E.,Bode, W.,Huber, R.,Empie, M.W.,Kato, I.,Laskowskijunior, M.
      (1982) J.Mol.Biol. 158: 515
    • Refined Crystal Structure of the Molecular Complex of Streptomyces Griseus Protease B, a Serine Protease, with the Third Domain of the Ovomucoid Inhibitor from Turkey
      Fujinaga, M.,Read, R.J.,Sielecki, A.,Ardelt, W.,Laskowskijunior, M.,James, M.N.G.
      (1982) Proc.Natl.Acad.Sci.USA 79: 4868



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OVOMUCOID THIRD DOMAIN
A
56Lophura nycthemeraMutation(s): 0 
Find proteins for P67954 (Lophura nycthemera)
Go to UniProtKB:  P67954
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 44.290α = 90.00
b = 21.150β = 107.00
c = 44.050γ = 90.00
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1985-06-11 
  • Released Date: 1985-11-08 
  • Deposition Author(s): Bode, W., Epp, O.

Revision History 

  • Version 1.0: 1985-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other