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- PDB-7qh3: Crystal structure of the anti-sigma factor RsfG from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 7qh3
TitleCrystal structure of the anti-sigma factor RsfG from Streptomyces tsukubaensis NRRL18488
ComponentsRsfG
KeywordsTRANSCRIPTION / anti-sigma / Streptomyces / sigma
Function / homologyDUF1579 domain-containing protein
Function and homology information
Biological speciesStreptomyces tsukubensis NRRL18488 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLeite, J.P. / Lourenco, F. / 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: RsfG
B: RsfG
C: RsfG
D: RsfG


Theoretical massNumber of molelcules
Total (without water)65,4074
Polymers65,4074
Non-polymers00
Water2,504139
1
A: RsfG


Theoretical massNumber of molelcules
Total (without water)16,3521
Polymers16,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RsfG


Theoretical massNumber of molelcules
Total (without water)16,3521
Polymers16,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RsfG


Theoretical massNumber of molelcules
Total (without water)16,3521
Polymers16,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RsfG


Theoretical massNumber of molelcules
Total (without water)16,3521
Polymers16,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.370, 61.130, 82.750
Angle α, β, γ (deg.)90.000, 106.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RsfG


Mass: 16351.823 Da / Num. of mol.: 4
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_011565, STSU_11555 / Production host: Escherichia coli (E. coli) / References: UniProt: I2N5H0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Ammonium phosphate dibasic; 0.1 M Tris hydrochloride pH 8.5; 0.5 M sodium phosphate dibasic dehydrate; 0.5 M potassium phosphate dibasic

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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 PILATUS 6M / Detector: PIXEL / Date: May 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→70.27 Å / Num. obs: 31236 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 43.61 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.087 / Num. unique obs: 3091

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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: 2.3→70.27 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1568 5.02 %
Rwork0.1925 29637 -
obs0.1949 31205 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.75 Å2 / Biso mean: 44.9133 Å2 / Biso min: 22.19 Å2
Refinement stepCycle: final / Resolution: 2.3→70.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 45 94 4356
Biso mean--42.58 51.36 -
Num. residues----545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.370.3441350.28182684281999
2.37-2.460.2961470.24422670281799
2.46-2.560.24961670.22392625279299
2.56-2.670.29561390.225126922831100
2.67-2.820.27271310.21682688281999
2.82-2.990.2381400.20342688282899
2.99-3.220.2471360.20512717285399
3.22-3.550.25751310.1762700283199
3.55-4.060.21251440.16682699284399
4.06-5.110.19721480.15382709285799
5.12-70.270.25981500.21282765291599

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