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- PDB-7qh5: The crystal structure of the sigma factor SigG1 from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 7qh5
TitleThe crystal structure of the sigma factor SigG1 from Streptomyces tsukubaensis NRRL18488
ComponentsRNA polymerase sigma factor
KeywordsTRANSCRIPTION / sigma factor / Streptomyces / ECF56
Function / homology
Function and homology information


response to stress / sigma factor activity / DNA-templated transcription initiation / DNA binding
Similarity search - Function
RNA polymerase sigma-G type, actinobacteria / 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 / SnoaL-like domain / SnoaL-like domain / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain ...RNA polymerase sigma-G type, actinobacteria / 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 / SnoaL-like domain / SnoaL-like domain / 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 / NTF2-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor
Similarity search - Component
Biological speciesStreptomyces tsukubensis NRRL18488 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLourenco, F. / Leite, J.P. / Gales, L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Crystal structures of Streptomyces tsukubaensis sigma factor SigG1 and anti-sigma RsfG.
Authors: Leite, J.P. / Lourenco, F. / Oliveira, R. / Sousa, S.F. / Mendes, M.V. / Gales, L.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase sigma factor
B: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5877
Polymers80,1262
Non-polymers4605
Water3,297183
1
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3394
Polymers40,0631
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2473
Polymers40,0631
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.639, 151.836, 128.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21B-519-

HOH

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Components

#1: Protein RNA polymerase sigma factor


Mass: 40063.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tsukubensis NRRL18488 (bacteria)
Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Gene: STSU_011570, STSU_11560 / Production host: Escherichia coli (E. coli) / References: UniProt: I2N5H1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M Sodium acetate trihydrate pH 7.0; 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→49.86 Å / Num. obs: 46348 / % possible obs: 99.9 % / Redundancy: 13.8 % / CC1/2: 0.999 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 3984 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.79 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 1990 4.33 %
Rwork0.2246 44017 -
obs0.2265 46007 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.43 Å2 / Biso mean: 41.8525 Å2 / Biso min: 21.56 Å2
Refinement stepCycle: final / Resolution: 2.2→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 30 183 5127
Biso mean--47.49 42.2 -
Num. residues----617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.40571230.37083083320699
2.26-2.320.40211430.32553070321399
2.32-2.380.3071450.2883083322899
2.38-2.460.3161360.25273121325799
2.46-2.550.32161450.242731403285100
2.55-2.650.28841390.246431003239100
2.65-2.770.31351450.253731333278100
2.77-2.920.32951360.250731363272100
2.92-3.10.26531460.23131373283100
3.1-3.340.28631510.231931253276100
3.34-3.680.22371390.211731773316100
3.68-4.210.21951510.178431873338100
4.21-5.30.22581420.175731953337100
5.3-49.790.2661490.224333303479100

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