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- PDB-6g1t: TraN, a repressor of an Enterococcus conjugative type IV secretio... -

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Basic information

Entry
Database: PDB / ID: 6g1t
TitleTraN, a repressor of an Enterococcus conjugative type IV secretion system
Components
  • (DNA (34-MER)) x 2
  • AM32
KeywordsDNA BINDING PROTEIN / Repressor / Protein-DNA complex / Type IV secretion system
Function / homologyisomerase activity / DNA / DNA (> 10) / AM32
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
Plasmid pIP501 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGoessweiner-Mohr, N. / Kohler, V. / Keller, W.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP27383 Austria
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: TraN: A novel repressor of an Enterococcus conjugative type IV secretion system.
Authors: Kohler, V. / Goessweiner-Mohr, N. / Aufschnaiter, A. / Fercher, C. / Probst, I. / Pavkov-Keller, T. / Hunger, K. / Wolinski, H. / Buttner, S. / Grohmann, E. / Keller, W.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AM32
E: DNA (34-MER)
D: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5454
Polymers35,3073
Non-polymers2381
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-30 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.770, 44.170, 56.460
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein AM32 / Enterococcus faecalis plasmid pAM-beta-1 copy number repressor (copF) / RepE (repE) / resolvase ...Enterococcus faecalis plasmid pAM-beta-1 copy number repressor (copF) / RepE (repE) / resolvase (res beta) / and type I topoisomerase (top beta) genes


Mass: 14396.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BVV5*PLUS
#2: DNA chain DNA (34-MER)


Mass: 10439.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Plasmid pIP501 (others)
#3: DNA chain DNA (34-MER)


Mass: 10470.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Plasmid pIP501 (others)
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: precipitant solution: 0.2 M Ammonium citrate tribasic, pH 7.0, 20 % (w/v) PEG 3,350 protein buffer: 25 mM HEPES pH 7.6, 75 mM Na2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→41.87 Å / Num. obs: 22900 / % possible obs: 96.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 1.93→2 Å

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P0Z

4p0z


Resolution: 1.93→41.87 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2125 --
Rwork0.1809 --
obs-22900 99.6 %
Refinement stepCycle: LAST / Resolution: 1.93→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 1251 15 121 2341

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