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- PDB-8b3z: SigE N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 8b3z
TitleSigE N-terminal Domain
ComponentsRNA polymerase sigma factor
KeywordsDNA BINDING PROTEIN / Sigma factor
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / sigma factor activity / DNA-templated transcription initiation / DNA binding
Similarity search - Function
RNA polymerase sigma-E type / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Sigma-70 factors family signature 1. / 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 ...RNA polymerase sigma-E type / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Sigma-70 factors family signature 1. / 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
Similarity search - Domain/homology
RNA polymerase sigma factor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsEvans, N.J. / Isaacson, R.L. / Collins, K.M. / Camp, A.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Microorganisms / Year: 2023
Title: Structural Analysis of Bacillus subtilis Sigma Factors.
Authors: Collins, K.M. / Evans, N.J. / Torpey, J.H. / Harris, J.M. / Haynes, B.A. / Camp, A.H. / Isaacson, R.L.
History
DepositionSep 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor
B: RNA polymerase sigma factor
C: RNA polymerase sigma factor
D: RNA polymerase sigma factor
E: RNA polymerase sigma factor
F: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)56,4066
Polymers56,4066
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-36 kcal/mol
Surface area24600 Å2
Unit cell
Length a, b, c (Å)81.953, 165.143, 98.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

21D-118-

HOH

31E-116-

HOH

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Components

#1: Protein
RNA polymerase sigma factor


Mass: 9401.021 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Bateq7PJ16_1703, SC09_Contig19orf01048 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1L9M9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.5 M Potassium thiocyanate 0.1 M Tris pH 8.5 7 mg.mL-1 in a 1:1 ratio
Temp details: Controlled Incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.379→63.39 Å / Num. obs: 27360 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 46.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.131 / Net I/σ(I): 13.4
Reflection shellResolution: 2.379→2.5 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1349 / CC1/2: 0.851 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
PHENIX1.16_3549refinement
DIALSdata reduction
DIALSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UGO

3ugo


Resolution: 2.38→63.39 Å / SU ML: 0.3459 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 1385 5.11 %
Rwork0.198 25730 -
obs0.2009 27115 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.12 Å2
Refinement stepCycle: LAST / Resolution: 2.38→63.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 94 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443626
X-RAY DIFFRACTIONf_angle_d0.57124899
X-RAY DIFFRACTIONf_chiral_restr0.0416599
X-RAY DIFFRACTIONf_plane_restr0.003625
X-RAY DIFFRACTIONf_dihedral_angle_d2.52242382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.460.43271360.3432493X-RAY DIFFRACTION97.19
2.46-2.560.39351160.31622539X-RAY DIFFRACTION98.77
2.56-2.680.27941420.27752511X-RAY DIFFRACTION98.51
2.68-2.820.30621310.2352562X-RAY DIFFRACTION99.41
2.82-30.27221640.21482523X-RAY DIFFRACTION99.19
3-3.230.25061290.2142585X-RAY DIFFRACTION99.67
3.23-3.550.23751290.18372596X-RAY DIFFRACTION99.45
3.55-4.070.2151310.17762573X-RAY DIFFRACTION99.38
4.07-5.120.20511400.15722643X-RAY DIFFRACTION100
5.12-63.390.27081670.18292705X-RAY DIFFRACTION99.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.37618702553-0.5995190163210.4142428291435.36601676444-0.1966530687543.770942169620.01914659876580.1486794099640.0771945694574-0.2632301461220.0470372327407-0.01580969113030.011646389562-0.0219967286269-0.0961139481170.3311237005520.1300361575410.05570424341350.317088771643-0.004258614060470.29384179455628.403408642226.170503027233.397367185
24.193634644020.705170747859-0.7395869261264.04960535818-1.683746753836.803366875380.0950558381113-0.210517371516-0.03953036110590.639001021954-0.1464100564370.2039984959650.09146141463320.211423615011-0.02513130199610.384680564223-0.2114296219780.03785613928950.4006472977150.0001992668308190.3065219308427.4811239029-26.096160247435.3466029062
32.398141456661.308133650240.7363468592835.8976365563-0.3568028532336.533884969670.05589415511540.07986570218550.364901506793-0.499365761564-0.09545530011210.7429684226380.0862292646326-0.34183708660.03275237828680.313378808179-0.0943276181628-0.03498646240250.415143241824-0.05535188218120.45322949100623.5393289647-25.347648606719.1812111978
46.208706803721.128892083910.7936751924028.103998951290.565717253273.68524957329-0.1261190656020.125120765229-0.098641221903-0.3362946819910.1763954365820.5881417027390.212850374682-0.3227743863840.05496731334610.229149632877-0.0609255204448-0.0133115310080.223362955640.03172384091450.21762016255430.7550424241-0.23478445258220.9736210862
52.99658875177-0.410254875119-0.3821228021724.51301932075-0.01687724085994.7231931959-0.1465189995080.5259810103920.441045088082-0.9814345115650.2190644982330.804715354527-0.192301927207-0.447975869102-0.03982134884290.390747906912-0.039300356813-0.1542270669430.4659209187220.1655417664740.51068234600727.978728695513.64026433711.5178311285
62.61782358532-0.92858990726-0.7185815037557.65991439619-1.321719122975.377636213370.272716892475-0.0236199934455-0.05211508819490.9593573700540.09391659335160.969714198837-0.422555978639-0.35655460504-0.1560260161810.4726883145350.1466980951380.1029520581890.3892536038740.09293617269890.53820122520220.876096739938.906170926741.2202817617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq -3:76)
2X-RAY DIFFRACTION2(chain B and resseq -2:74)
3X-RAY DIFFRACTION3(chain C and resseq 1:74)
4X-RAY DIFFRACTION4(chain D and resseq -3:74)
5X-RAY DIFFRACTION5(chain E and resseq 0:77)
6X-RAY DIFFRACTION6(chain F and resseq 0:76)

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