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Yorodumi- PDB-6pfv: Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhomb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pfv | ||||||
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Title | Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhombic crystal form | ||||||
Components |
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Keywords | TRANSCRIPTION / RsiG / WhiG / c-di-GMP / sigma / anti-sigma / Streptomyces | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) Streptomyces sp. PanSC19 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2020 Title: c-di-GMP Arms an Anti-sigma to Control Progression of Multicellular Differentiation in Streptomyces. Authors: Gallagher, K.A. / Schumacher, M.A. / Bush, M.J. / Bibb, M.J. / Chandra, G. / Holmes, N.A. / Zeng, W. / Henderson, M. / Zhang, H. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pfv.cif.gz | 669 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pfv.ent.gz | 564.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pfv_validation.pdf.gz | 591.4 KB | Display | wwPDB validaton report |
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Full document | 6pfv_full_validation.pdf.gz | 605.8 KB | Display | |
Data in XML | 6pfv_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 6pfv_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/6pfv ftp://data.pdbj.org/pub/pdb/validation_reports/pf/6pfv | HTTPS FTP |
-Related structure data
Related structure data | 6pfjSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19992.371 Da / Num. of mol.: 3 / Mutation: P91G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria) Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745 Gene: SVEN_3933 / Production host: Escherichia coli (E. coli) / References: UniProt: F2RFR7 #2: Protein | Mass: 30809.855 Da / Num. of mol.: 3 / Mutation: D38E, I97V, R144G, S150T, T159S, E162D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. PanSC19 (bacteria) / Gene: EDD98_3685 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N1Q704 #3: Chemical | ChemComp-C2E / Has ligand of interest | Y | |
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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: 2.6 Å3/Da / Density % sol: 52.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris Bicine pH 8.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 9% MPD, 10% PEG 1000 and 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→87.897 Å / Num. obs: 59828 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.053 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.99→3.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2129 / CC1/2: 0.447 / Rpim(I) all: 0.653 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PFJ Resolution: 3→87.897 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 33.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 256.36 Å2 / Biso mean: 112.7061 Å2 / Biso min: 32.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→87.897 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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Refinement TLS params. | Method: refined / Origin x: 54.1987 Å / Origin y: 32.2717 Å / Origin z: 15.9632 Å
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Refinement TLS group |
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