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- PDB-1sg5: Solution structure of Yaeo, a Rho-specific inhibitor of transcrip... -

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Basic information

Entry
Database: PDB / ID: 1sg5
TitleSolution structure of Yaeo, a Rho-specific inhibitor of transcription termination
Componentsorf, hypothetical protein
KeywordsSTRUCTURAL GENOMICS / TRANSCRIPTION / PROTEIN BINDING / a+b protein / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


regulation of termination of DNA-templated transcription / transcription antitermination
Similarity search - Function
Rof-like / Modulator of Rho-dependent transcription termination / Rof-like superfamily / Modulator of Rho-dependent transcription termination (ROF) / Rof/RNase P-like / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsGutierrez, P. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Solution Structure of YaeO, a Rho-specific Inhibitor of Transcription Termination
Authors: Gutierrez, P. / Kozlov, G. / Gabrielli, L. / Elias, D. / Osborne, M.J. / Gallouzi, I.E. / Gehring, K.
History
DepositionFeb 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: orf, hypothetical protein


Theoretical massNumber of molelcules
Total (without water)9,7091
Polymers9,7091
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 / 100structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein orf, hypothetical protein


Mass: 9708.901 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YaeO / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0AFW8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1223D 15N-separated NOESY
1312D NOESY
1442D NOESY
NMR detailsText: Structure determined using standar triple resonance and homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM YaeO, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3,90% H2O, 10% D2O90% H2O/10% D2O
22mM YaeO,U-15N, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
32mM YaeO,U-15N, 13C, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
42mM YaeO, 150mM phophate buffer, 2.0mM DTT; 0.1 mM NaN3, 100% D20100% D20
Sample conditionspH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker Biospinprocessing
XEASY1.3.13Bartelsdata analysis
ARIA1.1Nilgesdata analysis
CNS1.1Brungerrefinement
XwinNMR2.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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