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- PDB-1iw4: Solution structure of ascidian trypsin inhibitor -

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Basic information

Entry
Database: PDB / ID: 1iw4
TitleSolution structure of ascidian trypsin inhibitor
Componentstrypsin inhibitor
KeywordsPROTEIN BINDING / solution structure / ascidian / trypsin inhibitor / cystine-stabilized alpha-helical motif / disulfide bond / Kazal-type inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / 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 speciesHalocynthia roretzi (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsHemmi, H. / Yoshida, T. / Kumazaki, T. / Nemoto, N. / Hasegawa, J. / Nishioka, F. / Kyogoku, Y. / Yokosawa, H. / Kobayashi, Y.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure of ascidian trypsin inhibitor determined by nuclear magnetic resonance spectroscopy.
Authors: Hemmi, H. / Yoshida, T. / Kumazaki, T. / Nemoto, N. / Hasegawa, J. / Nishioka, F. / Kyogoku, Y. / Yokosawa, H. / Kobayashi, Y.
History
DepositionApr 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,0851
Polymers6,0851
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein trypsin inhibitor /


Mass: 6084.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halocynthia roretzi (invertebrata) / References: UniProt: P16589

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131E-COSY
141TOCSY
252TOCSY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-2.0mM ascidian trypsin inhibitor; 90% H2O, 10% D2O90% H2O/10% D2O
21.5-2.0mM ascidian trypsin inhibitor; D2OD2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.7 ambient 303 K
23.7 ambient 303 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 AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503
JEOL AJEOLA6004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglioprocessing
NMRPIPP4.3.2Garrettdata analysis
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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