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Yorodumi- PDB-7qh5: The crystal structure of the sigma factor SigG1 from Streptomyces... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qh5 | ||||||
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Title | The crystal structure of the sigma factor SigG1 from Streptomyces tsukubaensis NRRL18488 | ||||||
Components | RNA polymerase sigma factor | ||||||
Keywords | TRANSCRIPTION / 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 | ||||||
Biological species | Streptomyces tsukubensis NRRL18488 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lourenco, F. / Leite, J.P. / Gales, L. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qh5.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qh5.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qh5_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 7qh5_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 7qh5_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 7qh5_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/7qh5 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/7qh5 | HTTPS FTP |
-Related structure data
Related structure data | 7qh3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.2→2.28 Å / Num. unique obs: 3984 / CC1/2: 0.895 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.43 Å2 / Biso mean: 41.8525 Å2 / Biso min: 21.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→49.79 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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