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- PDB-2it7: Solution structure of the squash trypsin inhibitor EETI-II -

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Basic information

Entry
Database: PDB / ID: 2it7
TitleSolution structure of the squash trypsin inhibitor EETI-II
ComponentsTrypsin inhibitor 2
KeywordsPLANT PROTEIN / KNOTTIN / CYSTINE-KNOT / 3-10 HELIX / TRIPLE-STRANDED ANTI-PARALLEL BETA-SHEET
Function / homologyProteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily / serine-type endopeptidase inhibitor activity / extracellular region / Trypsin inhibitor 2
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, restrained molecular dynamics
AuthorsChiche, L. / Heitz, A. / Le-Nguyen, D.
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: Biochemistry / Year: 1989
Title: 1H 2D NMR and distance geometry study of the folding of Ecballium elaterium trypsin inhibitor, a member of the squash inhibitors family
Authors: Heitz, A. / Chiche, L. / Le-Nguyen, D. / Castro, B.
#2: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1989
Title: Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II
Authors: Chiche, L. / Gaboriaud, C. / Heitz, A. / Mornon, J.P. / Castro, B. / Kollman, P.A.
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 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_sheet.number_strands
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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)2,9071
Polymers2,9071
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 / Trypsin inhibitor II / EETI-II


Mass: 2907.464 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Ecballium elaterium
References: UniProt: P12071
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
14mM EETI-II, 90% H2O, 10% D2O90% H2O/10% D2O
24mM EETI-II, D2OD2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
12.71 atm285 K
22.71 atm300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
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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