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- PDB-1vd9: Solution structure of FMBP-1 tandem repeat 3 -

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Basic information

Entry
Database: PDB / ID: 1vd9
TitleSolution structure of FMBP-1 tandem repeat 3
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
AuthorsKawaguchi, K. / Yamaki, T. / Aizawa, T. / Takiya, S. / Demura, M. / Nitta, K.
CitationJournal: To be Published
Title: Solution structure of FMBP-1 tandem repeat 3
Authors: Kawaguchi, K. / Yamaki, T. / Aizawa, T. / Takiya, S. / Demura, M. / Nitta, K.
History
DepositionMar 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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
111DQF-COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.5mM peptide; pH 4 (10mM sodium phosphate buffer, 60mM NaCl); 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 60mM / pH: 4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
JEOL ALPHAJEOLALPHA6002

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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 184 restraints, 182 are NOE-derived distance constraints and 2 are dihedral angle restraints.
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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