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- PDB-1u0i: IAAL-E3/K3 heterodimer -

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Basic information

Entry
Database: PDB / ID: 1u0i
TitleIAAL-E3/K3 heterodimer
Components
  • IAAL-E3
  • IAAL-K3
KeywordsDE NOVO PROTEIN / coiled-coil
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, CHEMICAL-SHIFT AUTO -ASSIGNMENT, DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsLindhout, D.A. / Litowski, J.R. / Mercier, P. / Hodges, R.S. / Sykes, B.D.
CitationJournal: Biopolymers / Year: 2004
Title: NMR solution structure of a highly stable de novo heterodimeric coiled-coil
Authors: Lindhout, D.A. / Litowski, J.R. / Mercier, P. / Hodges, R.S. / Sykes, B.D.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IAAL-E3
B: IAAL-K3


Theoretical massNumber of molelcules
Total (without water)4,5722
Polymers4,5722
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 / 100back calculated data agree with experimental NOESY spectrum
Representative

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Components

#1: Protein/peptide IAAL-E3


Mass: 2285.651 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized using t-butyloxycarbonyl solid-phase technique
#2: Protein/peptide IAAL-K3


Mass: 2285.849 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized using t-butyloxycarbonyl solid-phase technique

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 1MM IAAL-E3/K3 COILED-COIL, NA-15N, PH 6.7, 100MM KCL, 50MM KPO4,90%/10% H2O/D2O, 23.1% TFE-D3
Sample conditionsIonic strength: 0.15 / pH: 6.7 / 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
Varian UNITYVarianUNITY5001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1GUNTERTrefinement
CYANA1GUNTERTstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, CHEMICAL-SHIFT AUTO -ASSIGNMENT, DISTANCE GEOMETRY, SIMULATED ANNEALING
Software ordinal: 1
Details: SOFTWARE USED WAS CYANA AND ITS INTEGRATED AUTO-ASSIGNMENT MODULE CANDID. THE CHEMICAL SHIFT IDENTIFICATION TOLERANCE AND TRANSPOSE ERRORS WERE SET TO 0.015 PPM IN BOTH PROTON DIMENSIONS. ...Details: SOFTWARE USED WAS CYANA AND ITS INTEGRATED AUTO-ASSIGNMENT MODULE CANDID. THE CHEMICAL SHIFT IDENTIFICATION TOLERANCE AND TRANSPOSE ERRORS WERE SET TO 0.015 PPM IN BOTH PROTON DIMENSIONS. STARTING WITH DISTANCE RESTRAINTS DERIVED FROM MANUALLY ASSIGNED NOE CROSS-PEAKS IN NMRVIEW, A TOTAL NUMBER OF 100 STRUCTURES WERE GENERATED PER CANDID ROUND WITH 8000 STEPS IN THE CYANA ANNEALING PROTOCOL. FOR EACH CANDID RUN, TALOS DERIVED ANGLE RESTRAINTS WERE INCORPORATED (WITH A MINIMUM ERROR SET MANUALLY TO 20 DEGREES) . THE BEST 20 LOW TARGET FUNCTION VALUE STRUCTURES OF CANDIDS FINAL ROUND WERE KEPT AS AN ENSEMBLE REPRESENTATION OF THE FAMILY OF GENERATED STRUCTURES.
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 20

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