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- PDB-1rik: E6-binding zinc finger (E6apc1) -

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Basic information

Entry
Database: PDB / ID: 1rik
TitleE6-binding zinc finger (E6apc1)
ComponentsE6apc1 peptide
KeywordsDE NOVO PROTEIN / E6-binding domain / zinc finger / human papillomavirus / HPV E6 protein
MethodSOLUTION NMR / dynamical annealing
AuthorsLiu, Y. / Liu, Z. / Androphy, E. / Chen, J. / Baleja, J.D.
CitationJournal: Biochemistry / Year: 2004
Title: Design and characterization of helical peptides that inhibit the E6 protein of papillomavirus.
Authors: Liu, Y. / Liu, Z. / Androphy, E. / Chen, J. / Baleja, J.D.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The peptide was N-terminally acetylated and C-terminally amidated, the coordinates do not ...SEQUENCE The peptide was N-terminally acetylated and C-terminally amidated, the coordinates do not reflect these modifications

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E6apc1 peptide


Theoretical massNumber of molelcules
Total (without water)3,5651
Polymers3,5651
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)50 / 50all calculated structures submitted
RepresentativeModel #33closest to the average

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Components

#1: Protein/peptide E6apc1 peptide


Mass: 3565.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D TOCSY
2212D NOESY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 to 3.0mM peptide, 10mM deuterated imidazole, 4mM ZnSO4, 1mM deuterated DTT, at pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
21.2 to 3.0mM peptide, 10mM deuterated imidazole, 4mM ZnSO4, 1mM deuterated DTT, at pH 6.0, 99.96% D2O99.96% D2O
Sample conditionsIonic strength: 10mM deuterated imidazole, 4mM ZnSO4, 1mM deuterated DTT,
pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker BioSpin GmbHcollection
XwinNMR3.5Bruker BioSpin GmbHprocessing
CNS1.1Brunger, et al.structure solution
CNS1.1Brunger, et al.refinement
RefinementMethod: dynamical annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 50

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