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- PDB-2n8c: Cystein knot with 2fp integrin avb6 cancer recognition site -

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Basic information

Entry
Database: PDB / ID: 2n8c
TitleCystein knot with 2fp integrin avb6 cancer recognition site
ComponentsCysteine knotCystine knot
KeywordsPROTEIN BINDING / DE NOVO PROTEIN / cancer / imaging
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsFilipp, F.V. / Kimura, R. / Tikole, S.
CitationJournal: To be Published
Title: Cystein knot with 2-FP label and integrin AvB6 cancer recognition site
Authors: Filipp, F.V. / Kimura, R. / Tikole, S.
History
DepositionOct 10, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Dec 27, 2023Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine knot


Theoretical massNumber of molelcules
Total (without water)3,9161
Polymers3,9161
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cysteine knot / Cystine knot


Mass: 3916.498 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1322D 1H-1H NOESY
1422D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM KNOT_2FP, 20 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
22 mM KNOT_2FP, 20 mM potassium phosphate, 5.5 M [U-2H] D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMKNOT_2FP-11
20 mMpotassium phosphate-21
2 mMKNOT_2FP-32
20 mMpotassium phosphate-42
5.5 MD2O-5[U-2H]2
Sample conditionsIonic strength: 20 / pH: 6.0 / Pressure: ambient / Temperature: 300 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
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeXDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.2Bruker Biospincollection
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 225 / NOE intraresidue total count: 2 / NOE long range total count: 97 / NOE medium range total count: 42 / NOE sequential total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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