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- PDB-1wnk: NMR Structure of FMBP-1 Tandem repeat 3 in 30%(V/V) TFE solution -

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Entry
Database: PDB / ID: 1wnk
TitleNMR Structure of FMBP-1 Tandem repeat 3 in 30%(V/V) TFE solution
ComponentsFibroin-Modulator-binding-protein-1
KeywordsTRANSCRIPTION / TANDEM REPEAT / N-CAP / DNA BINDING
Function / homology: / STPRs (score and three amino acid peptide repeats) / Fibroin-modulator-binding protein-1
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsYamaki, T. / Kawaguchi, K. / Aizawa, T. / Takiya, S. / Demura, M. / Nitta, K.
CitationJournal: To be Published
Title: NMR Structure of FMBP-1 Tandem repeat 3 in 30%(V/V) TFE Solution
Authors: Yamaki, T. / Kawaguchi, K. / Aizawa, T. / Takiya, S. / Demura, M. / Nitta, K.
History
DepositionAug 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroin-Modulator-binding-protein-1


Theoretical massNumber of molelcules
Total (without water)2,7101
Polymers2,7101
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)15 / 50structures with the lowest energy
RepresentativeModel #8lowest energy

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Components

#1: Protein/peptide Fibroin-Modulator-binding-protein-1 / FMBP-1


Mass: 2710.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT / References: UniProt: Q5FBS0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContents
11.5mM PEPTIDE; 70% H20, 30% TFE-D2
21.5mM PEPTIDE; 70% D20, 30% TFE-D3
Sample conditionspH: 3.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: JEOL ALPHA / Manufacturer: JEOL / Model: ALPHA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: the structures are based on a total of 266 restraints, 232 are NOE-derived distance constraints, 14 dihedral angle restraints, 20 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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