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- PDB-1t9e: NMR solution structure of a disulfide analogue of the cyclic sunf... -

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Basic information

Entry
Database: PDB / ID: 1t9e
TitleNMR solution structure of a disulfide analogue of the cyclic sunflower trypsin inhibitor SFTI-1
ComponentsTrypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / sunflower trypsin inhibitor / Disulfide mutant / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homologynegative regulation of endopeptidase activity / endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / protease binding / Trypsin inhibitor 1
Function and homology information
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / Structures were calculated using torsion angle dynamics, refined using cartesian dynamics, energy minimization in solvent using CNS.
AuthorsKorsinczky, M.L.J. / Clark, R.J. / Craik, D.J.
CitationJournal: Biochemistry / Year: 2005
Title: Disulfide bond mutagenesis and the structure and function of the head-to-tail macrocyclic trypsin inhibitor SFTI-1
Authors: Korsinczky, M.L.J. / Clark, R.J. / Craik, D.J.
History
DepositionMay 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Mar 26, 2025Group: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)1,5001
Polymers1,5001
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Mass: 1499.753 Da / Num. of mol.: 1 / Mutation: C3(ABA), C11(ABA) / Source method: obtained synthetically
Details: The peptide was synthesized using standard solid phase peptide synthesis methods using BOC chemistry. The peptide backbone was cyclicized in solution by addition of HBTU and DIEA which ...Details: The peptide was synthesized using standard solid phase peptide synthesis methods using BOC chemistry. The peptide backbone was cyclicized in solution by addition of HBTU and DIEA which resulted in the formation of a peptide bond between D14 and G1. The sequence of the peptide is naturally found in Helianthus Annus (sunflower)
Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
1422D TOCSY
1522D NOESY
162E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM peptide in 0.5 ml solvent90% H2O/10% D2O
210 mM peptide in 0.5 ml solvent100% D2O
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 290 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 DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
CNS1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENstructure solution
CNS1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
RefinementMethod: Structures were calculated using torsion angle dynamics, refined using cartesian dynamics, energy minimization in solvent using CNS.
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: 20

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