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- PDB-6jhe: Crystal Structure of Bacillus subtilis SigW domain 4 in complexed... -

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Basic information

Entry
Database: PDB / ID: 6jhe
TitleCrystal Structure of Bacillus subtilis SigW domain 4 in complexed with -35 element DNA
Components
  • DNA (5'-D(*AP*AP*AP*GP*GP*TP*TP*TP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*AP*AP*AP*CP*CP*TP*TP*T)-3')
  • ECF RNA polymerase sigma factor SigW
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / helix-turn-helix / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
RNA polymerase sigma-W, bacillaceae / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / 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-W, bacillaceae / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / ECF RNA polymerase sigma factor SigW
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
Model detailsCrystal Structure of Bacillus subtilis SigW domain 4 in complexed with -35 element DNA
AuthorsKwon, E. / Devkota, S.R. / Pathak, D. / Dahal, P. / Kim, D.Y.
CitationJournal: Plos One / Year: 2019
Title: Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis.
Authors: Kwon, E. / Devkota, S.R. / Pathak, D. / Dahal, P. / Kim, D.Y.
History
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECF RNA polymerase sigma factor SigW
B: DNA (5'-D(P*TP*TP*GP*AP*AP*AP*CP*CP*TP*TP*T)-3')
C: DNA (5'-D(*AP*AP*AP*GP*GP*TP*TP*TP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,0853
Polymers14,0853
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-18 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 61.620, 119.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ECF RNA polymerase sigma factor SigW / ECF sigma factor SigW / Alternative RNA polymerase sigma factor SigW / RNA polymerase sigma-W ...ECF sigma factor SigW / Alternative RNA polymerase sigma factor SigW / RNA polymerase sigma-W factor / Sigma-W factor


Mass: 7380.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sigW, ybbL, BSU01730 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q45585
#2: DNA chain DNA (5'-D(P*TP*TP*GP*AP*AP*AP*CP*CP*TP*TP*T)-3')


Mass: 3323.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*GP*GP*TP*TP*TP*CP*AP*A)-3')


Mass: 3381.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5 / Details: PEG 1500, isopropanol, CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 3013 / % possible obs: 99.4 % / Redundancy: 15.1 % / Biso Wilson estimate: 69.04 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 62.8
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.524 / Num. unique obs: 468 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIXdev_3051refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H27

2h27


Resolution: 3.101→29.842 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.36
RfactorNum. reflection% reflection
Rfree0.2895 140 5.16 %
Rwork0.2475 --
obs0.2496 2715 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168 Å2 / Biso mean: 69 Å2 / Biso min: 44.16 Å2
Refinement stepCycle: final / Resolution: 3.101→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms436 448 0 0 884
Num. residues----75
LS refinement shellResolution: 3.101→3.318 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2895 --
Rwork0.2475 2575 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: -3.941 Å / Origin y: -20.7209 Å / Origin z: -0.3 Å
111213212223313233
T0.9404 Å20.4036 Å2-0.2658 Å2-0.8324 Å2-0.2498 Å2--0.706 Å2
L4.1895 °2-0.4577 °2-0.9099 °2-2.9216 °20.0301 °2--3.7517 °2
S0.5396 Å °0.5417 Å °-0.6609 Å °-0.3748 Å °0.7213 Å °-0.6744 Å °1.1991 Å °1.3876 Å °-0.9586 Å °
Refinement TLS groupSelection details: all

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