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- PDB-1fyb: SOLUTION STRUCTURE OF C1-T1, A TWO-DOMAIN PROTEINASE INHIBITOR DE... -

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Basic information

Entry
Database: PDB / ID: 1fyb
TitleSOLUTION STRUCTURE OF C1-T1, A TWO-DOMAIN PROTEINASE INHIBITOR DERIVED FROM THE CIRCULAR PRECURSOR PROTEIN NA-PROPI FROM NICOTIANA ALATA
ComponentsPROTEINASE INHIBITORProtease inhibitor
KeywordsHydrolase Inhibitor / two-domain protein
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 / simulated annealing with torsion angle dynamics
AuthorsCraik, D.J. / Schirra, H.J. / Scanlon, M.J. / Anderson, M.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The solution structure of C1-T1, a two-domain proteinase inhibitor derived from a circular precursor protein from Nicotiana alata.
Authors: Schirra, H.J. / Scanlon, M.J. / Lee, M.C. / Anderson, M.A. / Craik, D.J.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)12,1001
Polymers12,1001
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 #4best secondary structure

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Components

#1: Protein PROTEINASE INHIBITOR / Protease inhibitor / NA-PROPI


Mass: 12099.669 Da / Num. of mol.: 1
Fragment: DOMAINS 1 AND 2 (C1 AND T1) FROM THE SIX-DOMAIN PRECURSOR PROTEIN NA-PROPI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana alata (Persian tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: Q40378

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
3333D 15N-separated NOESY
141DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and 3D heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM C1-T1, unlabeled90% H2O/10% D2O
21mM C1-T1, unlabeled99% D2O
31mM C1-T1, U-15N,13C90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 5.8 1 atm313 K
20 5.8 1 atm313 K
30 5.8 1 atm313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker ARXBrukerARX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
XEASY1.3.7Bartels, Xia, Billeter, Guentert, Wuethrichdata analysis
DYANA1.5Guentertstructure solution
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing with torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1193 constraints, 1039 are NOE-derived distance constraints, 82 dihedral angle restraints, and 72 hydrogen bond distance constraints
NMR representativeSelection criteria: best secondary structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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