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- PDB-5lme: Specific-DNA binding activity of the cross-brace zinc finger moti... -

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Basic information

Entry
Database: PDB / ID: 5lme
TitleSpecific-DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase
ComponentspiggyBac transposase
KeywordsTRANSCRIPTION / transposase piggyBac DNA-binding zinc-finger
Function / homologyPiggyBac transposable element-derived protein / Transposase IS4 / PiggyBac transposable element-derived protein domain-containing protein
Function and homology information
Biological speciesTrichoplusia ni (cabbage looper)
MethodSOLUTION NMR / simulated annealing
AuthorsMorellet, N. / Taylor, J.A. / Wieninger, S. / Moriau, S. / Li, X. / Lescop, E. / Mathy, N. / Bischerour, J. / Betermier, M. / Bardiaux, B. ...Morellet, N. / Taylor, J.A. / Wieninger, S. / Moriau, S. / Li, X. / Lescop, E. / Mathy, N. / Bischerour, J. / Betermier, M. / Bardiaux, B. / Nilges, M. / Craig, N.L. / Hickman, A.B. / Dyda, F. / Guittet, E.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase.
Authors: Morellet, N. / Li, X. / Wieninger, S.A. / Taylor, J.L. / Bischerour, J. / Moriau, S. / Lescop, E. / Bardiaux, B. / Mathy, N. / Assrir, N. / Betermier, M. / Nilges, M. / Hickman, A.B. / Dyda, ...Authors: Morellet, N. / Li, X. / Wieninger, S.A. / Taylor, J.L. / Bischerour, J. / Moriau, S. / Lescop, E. / Bardiaux, B. / Mathy, N. / Assrir, N. / Betermier, M. / Nilges, M. / Hickman, A.B. / Dyda, F. / Craig, N.L. / Guittet, E.
History
DepositionJul 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _entity.pdbx_fragment
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: piggyBac transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2483
Polymers5,1171
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 4000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide piggyBac transposase


Mass: 5117.271 Da / Num. of mol.: 1 / Fragment: C-terminal cysteine-rich domain / Source method: obtained synthetically / Source: (synth.) Trichoplusia ni (cabbage looper) / References: UniProt: Q27026
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D TOCSY
121isotropic22D NOESY
231isotropic12D DOSY
241isotropic22D HMQC
251isotropic12D HMQC

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Sample preparation

DetailsType: solution
Contents: 500 uM C-ter piggyBac, 1500 uM ZnCl2, 5 mM DTT, 200 mM sodium chloride, 10 % 100% labelling D2O, 90% H2O/10% D2O
Details: 500 microM, pH 6.5, 4eq ZnCl2, 5mM DTT, 200mM NaCl, 293K
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMC-ter piggyBacnatural abundance1
1500 uMZnCl2natural abundance1
5 mMDTTnatural abundance1
200 mMsodium chloridenatural abundance1
10 %D2O100% labelling1
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
1200 mMconditions_16.50.051 atm293 K
2200 mMcondition_26.7 pD1 atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIBrukerAVANCE II9502

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.3.1CCPNchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
Details: Two-state ensemble. Simultaneously optimized states are represented by successive models (1 and 2, 3 and 4 etc.), where odd numbers indicate state KF and even numbers state IF.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 24

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