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- PDB-2jyy: Solution structure of C8A/C37A-T1 from Nicotiana alata -

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Basic information

Entry
Database: PDB / ID: 2jyy
TitleSolution structure of C8A/C37A-T1 from Nicotiana alata
ComponentsProteinase inhibitor
KeywordsHYDROLASE INHIBITOR / protein / proteinase inhibitor / pot II inhibitor / free form
Function / homologyProteinase inhibitor I20 / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / serine-type endopeptidase inhibitor activity / 2-Layer Sandwich / Alpha Beta / Proteinase inhibitor
Function and homology information
Biological speciesNicotiana alata (Persian tobacco)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsStructure of a variant of the trypsin inhibitor T1 from N. alata in which the C8-C37 disulfide bond ...Structure of a variant of the trypsin inhibitor T1 from N. alata in which the C8-C37 disulfide bond has been deleted
AuthorsSchirra, H. / Guarino, R.F. / Anderson, M.A. / Craik, D.J.
CitationJournal: To be Published
Title: Selective removal of individual disulfide bonds in the Nicotiana alata proteinase inhibitor T1 reveals different stabilisation of the reactive site loop
Authors: Schirra, H. / Guarino, R.F. / Anderson, M.A. / Craik, D.J.
History
DepositionDec 20, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: 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_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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)5,6761
Polymers5,6761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Proteinase inhibitor


Mass: 5676.383 Da / Num. of mol.: 1 / Fragment: UNP residues 112-164 / Mutation: C8A, C37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana alata (Persian tobacco) / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q40378

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of a variant of the trypsin inhibitor T1 from N. alata in which the C8-C37 disulfide bond has been deleted
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1422D 1H-1H NOESY
1522D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.13 mM C8A/C37A-T1, 90% H2O/10% D2O90% H2O/10% D2O
20.13 mM C8A/C37A-T1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.13 mMC8A/C37A-T11
0.13 mMC8A/C37A-T12
Sample conditionsIonic strength: 0 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
GLXCCChristian Cieslarchemical shift assignment
GLXCCChristian Cieslardata analysis
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges, Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
MOLMOL2k.1Koradi, Billeter, Wuthrichdata analysis
ProcheckNMRLaskowski, MacArthurdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: First step: Standard Torsion angle dynamics simulated annealing within CNS_SOLVE (anneal.inp), Then refinement in explicit water according to Linge & Nilges.
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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