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- PDB-1xu0: Solution structure of Xenopus leavis prion protein -

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Basic information

Entry
Database: PDB / ID: 1xu0
TitleSolution structure of Xenopus leavis prion protein
Componentsprion proteinPRNP
KeywordsMEMBRANE PROTEIN / PRION / AMPHIBIAN / POLYMORPHISM / GLYCOPROTEIN
Function / homology
Function and homology information


: / protein homooligomerization / plasma membrane
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPerez, D.R. / Wuthrich, K.
CitationJournal: PROC.NATL.ACAD.SCI.USA / Year: 2005
Title: Prion protein NMR structures of chicken, turtle, and frog
Authors: Calzolai, L. / Lysek, D.A. / Perez, D.R. / Guntert, P. / Wuthrich, K.
History
DepositionOct 25, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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)15,0231
Polymers15,0231
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein prion protein / PRNP / xlPrP


Mass: 15022.910 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN(residues 98-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: prnp / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: Q5S1W7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY aliphatic region
1323D 13C-separated NOESY aromatic region

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, U-13C; 95% H2O, 5% D2O95% H2O/5% D2O
2U-15N, U-13C; 100% D2O100% D2O
Sample conditionsIonic strength: 10mM Sodium Acetat / pH: 4.5 / Pressure: ambient / Temperature: 293.15 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 AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6.01Guntert, P., Mumenthaler, C. & Wuthrich, K.structure solution
CANDIDHerrmann T, Guntert P, Wuthrich K.data analysis
OPALpR.KORADI,M.BILLITER,P.GUNTERTrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 2283 NOE-derived distance restraints.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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