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- PDB-1kma: NMR Structure of the Domain-I of the Kazal-type Thrombin Inhibito... -

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Basic information

Entry
Database: PDB / ID: 1kma
TitleNMR Structure of the Domain-I of the Kazal-type Thrombin Inhibitor Dipetalin
ComponentsDIPETALIN
KeywordsBLOOD CLOTTING / disulphide-rich small alpha+beta fold / Kazal-type
Function / homology
Function and homology information


negative regulation of coagulation / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Kazal-type serine protease inhibitor domain / 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
Serine protease inhibitor dipetalogastin
Similarity search - Component
Biological speciesDipetalogaster maximus (insect)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsSchlott, B. / Wohnert, J. / Icke, C. / Hartmann, M. / Ramachandran, R. / Guhrs, K.-H. / Glusa, E. / Flemming, J. / Gorlach, M. / Grosse, F. / Ohlenschlager, O.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Interaction of Kazal-type inhibitor domains with serine proteinases: biochemical and structural studies.
Authors: Schlott, B. / Wohnert, J. / Icke, C. / Hartmann, M. / Ramachandran, R. / Guhrs, K.H. / Glusa, E. / Flemming, J. / Gorlach, M. / Grosse, F. / Ohlenschlager, O.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPETALIN


Theoretical massNumber of molelcules
Total (without water)6,0911
Polymers6,0911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #16closest to the average

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Components

#1: Protein DIPETALIN / dipetalogastin


Mass: 6090.670 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN-I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dipetalogaster maximus (insect) / Plasmid: pMEX6 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: O96790

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Dipetalin-I U-15N94% H2O, 6% D2O; 50mM phosphate buffer; 100mM NaCl; 0.1mM EDTA
21.37mM Dipetalin-I U-15N,13C94% H2O, 6% D2O; 50mM phosphate buffer; 100mM NaCl; 0.1mM EDTA
Sample conditionspH: 6.68 / Pressure: ambient / Temperature: 288 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
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6Luginbuehlrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1122 distance constraints and 239 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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