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- PDB-1jr5: Solution Structure of the Anti-Sigma Factor AsiA Homodimer -

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Basic information

Entry
Database: PDB / ID: 1jr5
TitleSolution Structure of the Anti-Sigma Factor AsiA Homodimer
Components10 KDA Anti-Sigma Factor
KeywordsTRANSCRIPTION / All-alpha / Helix-Turn-Helix / Coiled-Coil
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 / simulated annealing, molecular dynamics, torsion angle, cartesian dynamics
AuthorsUrbauer, J.L. / Simeonov, M.F. / Bieber Urbauer, R.J. / Adelman, K. / Gilmore, J.M. / Brody, E.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions.
Authors: Urbauer, J.L. / Simeonov, M.F. / Urbauer, R.J. / Adelman, K. / Gilmore, J.M. / Brody, E.N.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Conserved Regions 4.1 and 4.2 of Sigma(70) Constitute the Recognition Sites for the Anti-Sigma Factor AsiA, and AsiA is a Dimer Free in Solution
Authors: Urbauer, J.L. / Adelman, K. / Bieber Urbauer, R.J. / Simeonov, M.F. / Gilmore, J.M. / Zolkiewski, M. / Brody, E.N.
#2: Journal: J.Biomol.NMR / Year: 1997
Title: Main-chain NMR assignments for AsiA
Authors: Urbauer, J.L. / Adelman, K. / Brody, E.N.
History
DepositionAug 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 10 KDA Anti-Sigma Factor / Audrey Stevens' Inhibitor


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: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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
232HNHA
3433D 13C F1-filtered F3-edited NOESY-HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM AsiA U-13C, 15N; 50 mM d4-acetate, 50 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
21.5 mM AsiA U-15N; 50 mM d4-acetate, 50 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
31.0 mM U-13C, 15N and 1.0 mM unlabeled; 50 mM d4-acetate, 50 mM KCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM d4-acetate, 50 mM KCl 6.3 ambient 298 K
250 mM d4-acetate, 50 mM KCl 6.3 ambient 298 K
350 mM d4-acetate, 50 mM KCl 6.3 ambient 298 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
Felix2000Molecular Simulationsprocessing
Felix2000Molecular Simulationsdata analysis
CNS1Brunger et alstructure solution
CNS1Brunger et alrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle, cartesian dynamics
Software ordinal: 1
Details: 2061 total NOE-based distance restraints including 34 hydrogen bond restraints and 36 intermolecular restraints, 153 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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