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- PDB-1lg4: NMR structure of the human doppel protein fragment 24-152 -

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Basic information

Entry
Database: PDB / ID: 1lg4
TitleNMR structure of the human doppel protein fragment 24-152
ComponentsPrion-like protein
KeywordsPrion Protein / prion / doppel / scrapie
Function / homology
Function and homology information


acrosome reaction / Post-translational modification: synthesis of GPI-anchored proteins / intracellular copper ion homeostasis / protein homooligomerization / copper ion binding / external side of plasma membrane / extracellular region / plasma membrane
Similarity search - Function
Prion-like protein Doppel / Prion-like protein Doppel / Prion/Doppel protein, beta-ribbon domain / 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
Prion-like protein doppel
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsLuhrs, T. / Riek, R. / Guntert, P. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: NMR Structure of the Human Doppel Protein
Authors: Luhrs, T. / Riek, R. / Guntert, P. / Wuthrich, K.
History
DepositionApr 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prion-like protein


Theoretical massNumber of molelcules
Total (without water)14,8441
Polymers14,8441
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 #1closest to the average

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Components

#1: Protein Prion-like protein / Doppel protein


Mass: 14843.668 Da / Num. of mol.: 1 / Fragment: hDpl(24-152)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Prnd / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: Q9UKY0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1323D 15N-separated NOESY
1432D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
113C,15N labeled hDpl(24-152)10% D2O, 90% H2O; 10 mM perdeuterated sodium acetate
215N labeled hDpl(24-152)10% D2O, 90% H2O; 10 mM perdeuterated sodium acetate
313C,15N labeled hDpl(24-152)99.9999% D2O; 10 mM perdeuterated sodium acetate
Sample conditionsIonic strength: 10 mM / pH: 4.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
XEASY1.5Bartels, C., Xia, T. H., Billeter, M., Guntert, P., and Wuthrich, K.data analysis
DYANA1.65Guntert, P., Herrmann, T., Mumenthaler, C., and Wuthrich, K.structure solution
OPALp1.3Luginbuhl, P., Guntert, P., Billeter, M., and Wuthrich, K.refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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