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- PDB-2k6x: Autoregulation of a Group 1 Bacterial Sigma Factor Involves the F... -

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Basic information

Entry
Database: PDB / ID: 2k6x
TitleAutoregulation of a Group 1 Bacterial Sigma Factor Involves the Formation of a Region 1.1- Induced Compacted Structure
ComponentsRNA polymerase sigma factor rpoD
KeywordsTRANSCRIPTION / sigma 1.1 / DNA-binding / Sigma factor / Transcription regulation
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Sigma-70 factor, region 1.1 / Annexin V; domain 1 / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 ...Sigma-70 factor, region 1.1 / Annexin V; domain 1 / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsSchwartz, E.C. / Shekhtman, A. / Dutta, K. / Pratt, M.R. / Cowburn, D. / Darst, S. / Muir, T.W.
CitationJournal: Chem.Biol. / Year: 2008
Title: Autoregulation of a Group 1 Bacterial Sigma Factor Involves the Formation of a Region 1.1 - Induced Compacted Structure
Authors: Schwartz, E.C. / Shekhtman, A. / Dutta, K. / Pratt, M.R. / Cowburn, D. / Darst, S. / Muir, T.W.
History
DepositionJul 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: RNA polymerase sigma factor rpoD


Theoretical massNumber of molelcules
Total (without water)8,3361
Polymers8,3361
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 512structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein RNA polymerase sigma factor rpoD / Sigma-A


Mass: 8336.333 Da / Num. of mol.: 1 / Fragment: UNP residues 29-96 / Mutation: S96G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rpoD, sigA, TM_1451 / Production host: Escherichia coli (E. coli) / References: UniProt: P77994

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D H(CCO)NH
1713D HBHA(CO)NH
1813D C(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 300-800 uM [U-100% 15N] sigma1.1, 300-800 uM [U-100% 13C; U-100% 15N] sigma1.1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMsigma1.1_1[U-100% 15N]1
300 uMsigma1.1_2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: Used Aria2.1, Intensities were converted into distance restraints using the symmetry ambiguous distance restraints (ADR) protocol
NMR constraintsProtein phi angle constraints total count: 54 / Protein psi angle constraints total count: 53
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 512 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0 Å

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