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- PDB-1iy5: Solution structure of wild type OMSVP3 -

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Basic information

Entry
Database: PDB / ID: 1iy5
TitleSolution structure of wild type OMSVP3
ComponentsOMSVP3
KeywordsHYDROLASE / solution structure / CSH motif / OMSVP3 / ovomucoid third domain / protease inhibitor
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)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsHemmi, H. / Kumazaki, T. / Yamazaki, T. / Kojima, S. / Yoshida, T. / Kyogoku, Y. / Katsu, M. / Yokosawa, H. / Miura, K. / Kobayashi, Y.
CitationJournal: BIOCHEMISTRY / Year: 2003
Title: Inhibitory Specificity Change of Ovomucoid Third Domain of the Silver Pheasant upon Introduction of an Engineered Cys14-Cys39 Bond
Authors: Hemmi, H. / Kumazaki, T. / Yamazaki, T. / Kojima, S. / Yoshida, T. / Kyogoku, Y. / Katsu, M. / Shinohara, F. / Yokosawa, H. / Miura, K. / Kobayashi, Y.
History
DepositionJul 23, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OMSVP3


Theoretical massNumber of molelcules
Total (without water)5,8611
Polymers5,8611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100low total energy and low deviation from mean structure
RepresentativeModel #11lowest energy

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Components

#1: Protein OMSVP3 / ovomucoid


Mass: 5860.613 Da / Num. of mol.: 1 / Fragment: third domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lophura nycthemera (Silver pheasant) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P67954
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 4.0mM OMSVP3; 90%H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglioprocessing
NMRPIPP4.3.2Garrettdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: low total energy and low deviation from mean structure
Conformers calculated total number: 100 / Conformers submitted total number: 15

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