[English] 日本語
Yorodumi- PDB-6g20: Crystal structure of a fluorescence optimized bathy phytochrome P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g20 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its functional Meta-F intermediate state. | ||||||
Components | Bacteriophytochrome protein | ||||||
Keywords | FLUORESCENT PROTEIN / SIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / META-F STATE / LIGHT ADAPTATION / BATHY PHYTOCHROME / PHOTOSENSORY CORE MODULE / OPTOGENETIC / FLOURESCENCE | ||||||
Function / homology | Function and homology information protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Schmidt, A. / Sauthof, L. / Szczepek, M. / Scheerer, P. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural snapshot of a bacterial phytochrome in its functional intermediate state. Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / ...Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / Krauss, N. / Lamparter, T. / Hildebrandt, P. / Scheerer, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g20.cif.gz | 405 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g20.ent.gz | 332.7 KB | Display | PDB format |
PDBx/mmJSON format | 6g20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g20_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6g20_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6g20_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6g20_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/6g20 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g20 | HTTPS FTP |
-Related structure data
Related structure data | 6g1yC 6g1zSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||||||||||||||||||||||||
2 |
| x 6||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56678.590 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Gene: SY94_2021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81 |
---|
-Non-polymers , 8 types, 345 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Chemical | ChemComp-PG0 / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.5 % |
---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion / Details: (NH4)2SO4, VAPOR DIFFUSION, TEMPERATURE 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→47.79 Å / Num. obs: 95000 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.16→2.28 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 13679 / CC1/2: 0.672 / Rpim(I) all: 0.409 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G1Z Resolution: 2.16→158.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.027 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.886 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.16→158.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|