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- PDB-1tkv: Solution Structure of T4 AsiA Dimer -

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Basic information

Entry
Database: PDB / ID: 1tkv
TitleSolution Structure of T4 AsiA Dimer
Components10 kDa anti-sigma factor
KeywordsTRANSCRIPTION / anti-sigma / homodimer
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, restrained energy minimization
AuthorsLambert, L.J. / Schirf, V. / Demeler, B. / Cadene, M. / Werner, M.H.
CitationJournal: Embo J. / Year: 2001
Title: Flipping a genetic switch by subunit exchange
Authors: Lambert, L.J. / Schirf, V. / Demeler, B. / Cadene, M. / Werner, M.H.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJun 22, 2004ID: 1KA3
Revision 1.0Jun 22, 2004Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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
B: 10 kDa anti-sigma factor


Theoretical massNumber of molelcules
Total (without water)21,2082
Polymers21,2082
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)23 / 100structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #1lowest energy

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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.: 2
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
131NH residual dipolar couplings in Pf1 at 9 mg/ml

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 50 mM NaCl, 2 mM CHAPS, 50 mM sodium azide
Solvent system: 97% H2O, 3% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.2 / 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 AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3Clore and Schweitersrefinement
NMRPipe2.2Delagliodata analysis
RefinementMethod: dynamical simulated annealing, restrained energy minimization
Software ordinal: 1
Details: Initial folding from a fully extended template using NOEs, dihedral restraints and NH residual dipolar couplings. Iterative refinement with NOESY data.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 23

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