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- PDB-1id7: SOLUTION STRUCTURE OF SYR6 -

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Basic information

Entry
Database: PDB / ID: 1id7
TitleSOLUTION STRUCTURE OF SYR6
ComponentsSYR6
KeywordsANTIVIRAL PROTEIN / SYR6
Function / homology:
Function and homology information
MethodSOLUTION NMR / 4D simulated annealing
Model type detailsminimized average
AuthorsSato, A. / Kawaguchi, K. / Kimura, K. / Tanimura, R. / Sone, S.
CitationJournal: To be Published
Title: A peptide mimetic of IFN, the first proof of a small peptidic agonist for heterodimeric cytokine receptor
Authors: Sato, A. / Kawaguchi, K. / Kimura, K. / Tanimura, R. / Sone, S.
History
DepositionApr 4, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: 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: 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYR6


Theoretical massNumber of molelcules
Total (without water)1,7851
Polymers1,7851
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)1 / 750Average structure of the 11 structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide SYR6


Mass: 1784.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: GB : 15076606

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2.0mM SYR6; deuterated dimethyl sulfoxide 100% / Solvent system: deuterated dimethyl sulfoxide 100%
Sample conditionsPressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
EMBOSS5Morikawa, S. et. al.structure solution
EMBOSS5Morikawa, S. et. al.refinement
RefinementMethod: 4D simulated annealing / Software ordinal: 1
Details: The average structure of the 11 structures that are based on 66 NOE-derived distance constraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: Average structure of the 11 structures with the least restraint violations
Conformers calculated total number: 750 / Conformers submitted total number: 1

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