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- PDB-1xyk: NMR Structure of the canine prion protein -

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Basic information

Entry
Database: PDB / ID: 1xyk
TitleNMR Structure of the canine prion protein
Componentsprion protein
KeywordsUNKNOWN FUNCTION / PrP / prion / Prnp / cPrP
Function / homology
Function and homology information


side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily ...Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLysek, D.A. / Schorn, C. / Esteve-Moya, V. / Herrmann, T. / Wuthrich, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Prion protein NMR structures of cats, dogs, pigs, and sheep
Authors: Lysek, D.A. / Schorn, C. / Nivon, L.G. / Esteve-Moya, V. / Christen, B. / Calzolai, L. / von Schroetter, C. / Fiorito, F. / Herrmann, T. / Guntert, P. / Wuthrich, K.
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: prion protein


Theoretical massNumber of molelcules
Total (without water)13,0851
Polymers13,0851
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)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein prion protein


Mass: 13084.538 Da / Num. of mol.: 1 / Fragment: cPrP C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O46501

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using standard 3D techniques

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Sample preparation

DetailsContents: 1mM cPrP U-15N, 13C; 10mM acetate / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 / pH: 4.5 / 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: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6.2Gntertstructure solution
CANDID1Herrmannrefinement
ATNOS1Herrmannrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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