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- PDB-2it8: Solution structure of a linear analog of the cyclic squash trypsi... -

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Basic information

Entry
Database: PDB / ID: 2it8
TitleSolution structure of a linear analog of the cyclic squash trypsin inhibitor MCoTI-II
ComponentsTrypsin inhibitor 2
KeywordsPLANT PROTEIN / PLANT PROTEIN ANALOG / KNOTTIN / CYSTINE-KNOT / 3-10 HELIX / TRIPLE-STRANDED ANTI-PARALLEL BETA-SHEET
Function / homology
Function and homology information


negative regulation of serine-type endopeptidase activity / serine-type endopeptidase inhibitor activity / defense response / extracellular region
Similarity search - Function
Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily
Similarity search - Domain/homology
Biological speciesMomordica cochinchinensis (spiny bitter cucumber)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, restrained molecular dynamics
AuthorsAvrutina, O. / Chiche, L. / Diederichsen, U. / Heitz, A. / Kolmar, H.
Citation
Journal: To be Published
Title: Knottin cyclization: Structure and stability of cyclic and linear squash inhibitors do not differ significantly
Authors: Heitz, A. / Avrutina, O. / Le-Nguyen, D. / Diederichsen, U. / Hernandez, J.F. / Gracy, J. / Kolmar, H. / Chiche, L.
#1: Journal: Biol.Chem. / Year: 2005
Title: Trypsin inhibition by macrocyclic and open-chain variants of the squash inhibitor MCoTI-II
Authors: Avrutina, O. / Schmoldt, H.U. / Gabrijelcic-Geiger, D. / Le-Nguyen, D. / Sommerhoff, C.P. / Diederichsen, U. / Kolmar, H.
#2: Journal: Eur.J.Org.Chem. / Year: 2004
Title: Fmoc-assisted synthesis of a 29-residue cystine-knot trypsin inhibitor containing a guanyl amino acid at the P1-position
Authors: Avrutina, O. / Schmoldt, H.U. / Kolmar, H. / Diederichsen, U.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 700SHEET DETERMINATION METHOD: AUTHOR-DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor 2


Theoretical massNumber of molelcules
Total (without water)3,0781
Polymers3,0781
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)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Trypsin inhibitor 2 / MCoTI-II / Trypsin inhibitor II


Mass: 3077.700 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Momordica cochinchinensis (spiny bitter cucumber)
References: UniProt: P82409
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
2312D NOESY
2412D TOCSY
2522D 1H-13C HSQC
2622D NOESY
2722D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM peptide, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 mM peptide, D2OD2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
131 atm285 K
231 atm300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1brukercollection
XwinNMR3.1brukerprocessing
CYANA2.1Guntert, P. et al.structure solution
Amber8Case, D.A. et al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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