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- PDB-2ovo: THE CRYSTAL AND MOLECULAR STRUCTURE OF THE THIRD DOMAIN OF SILVER... -

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Basic information

Entry
Database: PDB / ID: 2ovo
TitleTHE CRYSTAL AND MOLECULAR STRUCTURE OF THE THIRD DOMAIN OF SILVER PHEASANT OVOMUCOID (OMSVP3)
ComponentsOVOMUCOID THIRD DOMAIN
KeywordsPROTEINASE INHIBITOR (KAZAL)
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
: / Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...: / Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLophura nycthemera (Silver pheasant)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsBode, W. / Epp, O.
Citation
Journal: Eur.J.Biochem. / Year: 1985
Title: The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3).
Authors: Bode, W. / Epp, O. / Huber, R. / Laskowski Jr., M. / Ardelt, W.
#1: Journal: Biochemistry / Year: 1982
Title: Thermodynamics and Kinetics of Single Residue Replacements in Avian Ovomucoid Third Domains. Effect on Inhibitor Interactions with Serine Proteinases
Authors: Empie, M.W. / Laskowskijunior, M.
#2: Journal: Biochemistry / Year: 1983
Title: Structure of the Complex of Streptomyces Griseus Protease B and the Third Domain of the Turkey Ovomucoid Inhibitor at 1.8-Angstroms Resolution
Authors: Read, R.J. / Fujinaga, M. / Sielecki, A.R. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic Refinement of Japanese Quail Ovomucoid, a Kazal-Type Inhibitor, and Model Building Studies of Complexes with Serine Proteases
Authors: Papamokos, E. / Weber, E. / Bode, W. / Huber, R. / Empie, M.W. / Kato, I. / Laskowskijunior, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: 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
Authors: Fujinaga, M. / Read, R.J. / Sielecki, A. / Ardelt, W. / Laskowskijunior, M. / James, M.N.G.
#5: Journal: Colloq.Ges.Biol.Chem. / Year: 1981
Title: Correlation of Amino Acid Sequence with Inhibitor Activity and Specificity of Protein Inhibitors of Serine Proteinases
Authors: Laskowskijunior, M. / Empie, M.W. / Kato, I. / Kohr, W.J. / Ardelt, W. / Bogardjunior, W.C. / Weber, E. / Papamokos, E. / Bode, W. / Huber, R.
#6: Journal: J.Mol.Biol. / Year: 1981
Title: Crystallization, Crystal Structure Analysis and Molecular Model of the Third Domain of Japanese Quail Ovomucoid, a Kazal Type Inhibitor
Authors: Weber, E. / Papamokos, E. / Bode, W. / Huber, R. / Kato, I. / Laskowskijunior, M.
History
DepositionJun 11, 1985Processing site: BNL
Revision 1.0Nov 8, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_validate_rmsd_angle
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OVOMUCOID THIRD DOMAIN


Theoretical massNumber of molelcules
Total (without water)6,0451
Polymers6,0451
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.290, 21.150, 44.050
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE 12 IS A CIS-PROLINE.

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Components

#1: Protein OVOMUCOID THIRD DOMAIN


Mass: 6044.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lophura nycthemera (Silver pheasant) / References: UniProt: P67954
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.63 Å3/Da / Density % sol: 24.63 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown / PH range low: 7 / PH range high: 6
Components of the solutions
*PLUS
Conc.: 1.0 M / Common name: ammonium sulfate

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Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 4837 / % possible obs: 75 % / Rmerge(I) obs: 0.035

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.5→7 Å / Rfactor Rwork: 0.199
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms418 0 0 31 449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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