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- PDB-2kfl: Tammar Wallaby Prion Protein (121-230) -

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Basic information

Entry
Database: PDB / ID: 2kfl
TitleTammar Wallaby Prion Protein (121-230)
ComponentsMajor prion protein
KeywordsUNKNOWN FUNCTION / Tammar Wallaby PrP / Cell membrane / Membrane / Prion
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 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 speciesMacropus eugenii (tammar wallaby)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsChristen, B. / Hornemann, S. / Damberger, F.F. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Prion Protein NMR Structure from Tammar Wallaby (Macropus eugenii) Shows that the beta2-alpha2 Loop Is Modulated by Long-Range Sequence Effects.
Authors: Christen, B. / Hornemann, S. / Damberger, F.F. / Wuthrich, K.
History
DepositionFeb 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)13,1501
Polymers13,1501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Major prion protein


Mass: 13149.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macropus eugenii (tammar wallaby) / Gene: PRNP / Production host: Escherichia coli (E. coli) / References: UniProt: Q58YZ3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HNCA
1413D HNCO
1513D HN(CA)CO
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D (H)CCH-COSY
1913D H(CCCO)NH
11013D (H)C(CCO)NH

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Sample preparation

DetailsContents: 10 mM [U-100% 2H] sodium acetate, 1.5 mM [U-99% 13C; U-99% 15N] protein, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium acetate[U-100% 2H]1
1.5 mMentity[U-99% 13C; U-99% 15N]1
0.02 %sodium azide1
Sample conditionsIonic strength: 0.01 / pH: 4.5 / Pressure: ambient / Temperature: 293.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichdata analysis
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichpeak picking
ATNOS/CANDID1.2Herrmann, Guntert and Wuthrichchemical shift assignment
DYANA1.0.3Guntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
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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