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- PDB-1pm6: Solution Structure of Full-Length Excisionase (Xis) from Bacterio... -

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Basic information

Entry
Database: PDB / ID: 1pm6
TitleSolution Structure of Full-Length Excisionase (Xis) from Bacteriophage HK022
ComponentsExcisionase
KeywordsGENE REGULATION / ANTIPARALLEL BETA-SHEET / WINGED-HELIX / CIS-TRANS-TRANS TRIPROLINE
Function / homology
Function and homology information


provirus excision / DNA recombination / DNA binding
Similarity search - Function
Excisionase (Xis) protein / Excisionase-like / Excisionase-like superfamily / Excisionase-like protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage HK022 (virus)
MethodSOLUTION NMR / energy minimization
AuthorsRogov, V.V. / Luecke, C. / Muresanu, L. / Wienk, H. / Kleinhaus, I. / Werner, K. / Loehr, F. / Pristovsek, P. / Rueterjans, H.
CitationJournal: Eur.J.Biochem. / Year: 2003
Title: Solution structure and stability of the full-length excisionase from bacteriophage HK022.
Authors: Rogov, V.V. / Lucke, C. / Muresanu, L. / Wienk, H. / Kleinhaus, I. / Werner, K. / Lohr, F. / Pristovsek, P. / Ruterjans, H.
History
DepositionJun 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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


Theoretical massNumber of molelcules
Total (without water)8,6381
Polymers8,6381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
Representative

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Components

#1: Protein Excisionase


Mass: 8638.055 Da / Num. of mol.: 1 / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage HK022 (virus) / Genus: Lambda-like viruses / Gene: XIS / Plasmid: pPG14_C28S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: P68927

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3112D NOESY
3222D NOESY
3333D 15N-separated NOESY
3443D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance and homonuclear NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Xis, 50 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM EDTA disodium salt, 0.03% sodium azide, 100% D2O100% D2O
21 mM Xis, 50 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM EDTA disodium salt, 0.03 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
31 mM Xis U-15N, 50 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM EDTA disodium salt, 0.03 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
41 mM Xis U-13C,15N, 50 mM sodium phosphate, 100 mM sodium chloride, 0.2 mM EDTA disodium salt, 0.03 % sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 303 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
AURELIA2.7.5Brukerdata analysis
Felix97Accelrysdata analysis
DYANA1.5Guentertstructure solution
Discover2.98Accelrysrefinement
Procheck-NMR3.4.4Laskowskirefinement
RefinementMethod: energy minimization / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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