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- PDB-1m8c: SOLUTION STRUCTURE OF THE T State OF TURKEY OVOMUCOID AT PH 2.5 -

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Basic information

Entry
Database: PDB / ID: 1m8c
TitleSOLUTION STRUCTURE OF THE T State OF TURKEY OVOMUCOID AT PH 2.5
ComponentsOvomucoid
KeywordsHYDROLASE INHIBITOR / OMTKY3 CONFORMATIONAL TRANSITION T STATE / CIS-TRANS ISOMERIZATION
Function / homology
Function and homology information


molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ovomucoid / Ovomucoid
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsSong, J. / Laskowski Jr., M. / Qasim, M.A. / Markley, J.L.
CitationJournal: Biochemistry / Year: 2003
Title: Two conformational states of Turkey ovomucoid third domain at low pH: three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics.
Authors: Song, J. / Laskowski Jr, M. / Qasim, M.A. / Markley, J.L.
History
DepositionJul 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ovomucoid


Theoretical massNumber of molelcules
Total (without water)6,0451
Polymers6,0451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ovomucoid /


Mass: 6044.783 Da / Num. of mol.: 1
Fragment: RESIDUES 130-185; KAZAL-LIKE 3 (INHIBIT CHYMOTRYPIN, ELASTASE, ETC.)
Mutation: P14D / Source method: obtained synthetically
Details: The sequence for Ovomucoid fragment was chemically synthesized. It occurs naturally in Meleagris gallopavo (Common turkey).
References: UniProt: P01004, UniProt: P68390*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
1422D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM90% H2O/10% D2O
21 mM100% D2O
Sample conditionsIonic strength: no salt added / pH: 2.5 / 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 DMXBrukerDMX7501
Bruker AMXBrukerAMX6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionClassification
XwinNMR3.2collection
Felix95processing
Sparky3.72data analysis
DYANA1.5structure solution
DYANA1.5refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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