[English] 日本語
Yorodumi- PDB-6pfj: Structure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pfj | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 crystal form | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / sigma / anti-sigma / c-di-GMP / developmental switch | ||||||
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 / SAD / Resolution: 2.08 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pfj.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pfj.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pfj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pfj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6pfj_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 6pfj_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/6pfj ftp://data.pdbj.org/pub/pdb/validation_reports/pf/6pfj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19992.371 Da / Num. of mol.: 1 / 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: 30924.023 Da / Num. of mol.: 1 / Mutation: D38E, 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 | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
---|---|
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, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→79.8 Å / Num. obs: 53003 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.08→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.4 / % possible all: 94 |
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.08→79.75 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 26.47
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→79.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -26.24 Å / Origin y: -3.0781 Å / Origin z: -0.2581 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |