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- PDB-1tl6: Solution structure of T4 bacteriphage AsiA monomer -

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Basic information

Entry
Database: PDB / ID: 1tl6
TitleSolution structure of T4 bacteriphage AsiA monomer
Components10 kDa anti-sigma factor
KeywordsTRANSCRIPTION / Asia / T4 bacteriophage
Function / homologyAnti-sigma factor AsiA / Anti-Sigma Factor A / Anti-Sigma Factor A / Anti-Sigma Factor A superfamily / Anti-Sigma Factor A / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / 10 kDa anti-sigma factor
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodSOLUTION NMR / dynamical simulated annealing with restrained energy minimization
AuthorsLambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
CitationJournal: Embo J. / Year: 2004
Title: T4 AsiA blocks DNA recognition by remodeling sigma70 region 4
Authors: Lambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: 10 kDa anti-sigma factor


Theoretical massNumber of molelcules
Total (without water)10,6041
Polymers10,6041
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)22 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein 10 kDa anti-sigma factor / Audrey Stevens' inhibitor / 10 kDa RNA polymerase-associated protein


Mass: 10604.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: ASIA / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-SI / References: UniProt: P32267

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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
131residual dipolar couplings in Pf1 phage @ 9 mg/ml
NMR detailsText: NH and CalphaH RDC values measured

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Sample preparation

DetailsContents: 0.7 mM AsiA, phosphate buffered saline,2 mM CHAPS / Solvent system: 97% H2O, 3% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 298 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 DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX8003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3Clore and Schweitersrefinement
NMRPipe2.2Delagliodata analysis
RefinementMethod: dynamical simulated annealing with restrained energy minimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 22

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