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- PDB-1y6u: The Structure of the Excisionase (Xis) Protein from Conjugative T... -

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Basic information

Entry
Database: PDB / ID: 1y6u
TitleThe Structure of the Excisionase (Xis) Protein from Conjugative Transposon Tn916 Provides Insights into the Regulation of Heterobivalent Tyrosine Recombinases
ComponentsExcisionase from transposon Tn916
KeywordsDNA BINDING PROTEIN / DNA architectural protein / Tyrosine recombinase / Excisionase / Winged-helix protein / Conjugative transposon
Function / homology
Function and homology information


DNA integration / DNA recombination
Similarity search - Function
Molybdopterin biosynthesis moea protein, domain 2 - #50 / Excisionase from transposon Tn916 / Transposon Tn1545/Tn916, excisionase / Excisionase from transposon Tn916 / Molybdopterin biosynthesis moea protein, domain 2 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / Hybrid distance geometry, simulated annealing calculations
AuthorsAbbani, M. / Iwahara, M. / Clubb, R.T.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The structure of the excisionase (xis) protein from conjugative transposon tn916 provides insights into the regulation of heterobivalent tyrosine recombinases
Authors: Abbani, M. / Iwahara, M. / Clubb, R.T.
History
DepositionDec 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Excisionase from transposon Tn916


Theoretical massNumber of molelcules
Total (without water)8,3901
Polymers8,3901
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Excisionase from transposon Tn916 / xis


Mass: 8389.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: xis / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): RJ3386 (BL21-DE3) / References: UniProt: Q79DA1

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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
1314D 13C/15N-separated NOESY
141HNCA-J
151HNHA

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Sample preparation

DetailsContents: 1 mM 15N/13C labeled Xis, 30 mM NaOAc, 60 mM NaCl, 93% H2O, 7% D2O
Solvent system: 30 mM NaOAc, pH 4.5, 60 mM NaCl, 93% H2O, 7% D2O
Sample conditionsIonic strength: 60 mM NaCl / pH: 4.5 / Pressure: Ambient / Temperature: 303 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
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
X-PLOR3.1processing
NMRPipesgi6xprocessing
PIPP4.3.5data analysis
XPLOR-NIHrefinement
RefinementMethod: Hybrid distance geometry, simulated annealing calculations
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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