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- PDB-2jot: Nuclear Magnetic Resonance Studies on Huwentoxin-XI from the Chin... -

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Basic information

Entry
Database: PDB / ID: 2jot
TitleNuclear Magnetic Resonance Studies on Huwentoxin-XI from the Chinese Bird Spider Ornithoctonus huwena
ComponentsHuwentoxin-11
KeywordsTOXIN / Proteinase inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type kappaPI-theraphotoxin-Hs1a
Similarity search - Component
Biological speciesOrnithoctonus huwena (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsPeng, K. / Liang, S.
CitationJournal: To be Published
Title: Nuclear Magnetic Resonance Studies on Huwentoxin-XI from the Chinese Bird Spider Ornithoctonus huwena
Authors: Liang, S.
History
DepositionMar 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Huwentoxin-11


Theoretical massNumber of molelcules
Total (without water)6,1831
Polymers6,1831
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Huwentoxin-11 / / Huwentoxin-XI / HwTx-XI


Mass: 6183.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithoctonus huwena (Chinese earth tiger)
Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S-78 / References: UniProt: P68425

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC
1412D 1H-15N HSQC
1513D 1H-15N TOCSY
1613D 1H-15N NOESY

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Sample preparation

DetailsContents: 5 mM [U-100% 15N] Huwentoxin-xi, 50mM K2HPO4-KH2PO4 buffer (adjust pH value to 4.0 using H3PO4), small amount of azide for stabilization, sodium 2, 2-dimethyl-2- silapentane-5-sulfonate (DSS), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 5 mM / Component: Huwentoxin-xi / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 4.0 / Pressure: ambient / Temperature: 303 K

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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 AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, distance geometry / 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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