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- PDB-1ku7: Crystal Structure of Thermus aquatics RNA Polymerase SigmaA Subun... -

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Basic information

Entry
Database: PDB / ID: 1ku7
TitleCrystal Structure of Thermus aquatics RNA Polymerase SigmaA Subunit Region 4 Bound to-35 Element DNA
Components
  • 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'
  • 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'
  • sigma factor sigA
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / double-helix / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
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 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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCampbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2002
Title: Structure of the bacterial RNA polymerase promoter specificity sigma subunit.
Authors: Campbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A.
History
DepositionJan 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 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
B: 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'
C: 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'
A: sigma factor sigA
D: sigma factor sigA


Theoretical massNumber of molelcules
Total (without water)24,1414
Polymers24,1414
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.180, 62.650, 94.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'


Mass: 3342.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: -35 Element DNA
#2: DNA chain 5'-D(*CP*CP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3'


Mass: 3324.184 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein sigma factor sigA


Mass: 8737.127 Da / Num. of mol.: 2 / Fragment: region 4 (residues 366-438) / Mutation: L386M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EZJ8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES, PEG 4000, magnesium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 400011
3magnesium acetate11
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
20.1 MMES1reservoirpH6.0
32.4 Mammonium sulfate1reservoir
420 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 9, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 8898 / Num. obs: 8698 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 %
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å / Num. obs: 7801 / Num. measured all: 29108 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→25 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.293 484 -
Rwork0.255 --
all0.255 8898 -
obs0.255 8698 97.8 %
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 442 0 67 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00696
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00696
X-RAY DIFFRACTIONc_angle_deg1.3

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