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- PDB-1u5l: Solution Structure of the turtle prion protein fragment (121-226) -

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Basic information

Entry
Database: PDB / ID: 1u5l
TitleSolution Structure of the turtle prion protein fragment (121-226)
Componentsprion protein
KeywordsMEMBRANE PROTEIN / Prnp / PrP / prion / TSE
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / 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 / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain ...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 / 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 speciesTrachemys scripta (red-eared slider turtle)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLysek, D.A. / Calzolai, L. / Guntert, P. / 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
DepositionJul 28, 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)12,6111
Polymers12,6111
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein prion protein


Mass: 12610.997 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (residues 121-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trachemys scripta (red-eared slider turtle)
Gene: Prnp / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I9C0

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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

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM turtle prion protein U-15N,13C; 10mM sodium acetate, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM turtle prion protein U-15N,13C; 10mM sodium acetate, 99% D2O99% D2O
Sample conditionsIonic strength: 10mM / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6Guentertstructure solution
DYANA6Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1632 restraints, 1522 are NOE-derived distance constraints, 110 dihedral angle restraints, 109
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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