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Yorodumi- PDB-4r6l: Crystal structure of bacteriophytochrome RpBphP2 from photosynthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r6l | ||||||
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Title | Crystal structure of bacteriophytochrome RpBphP2 from photosynthetic bacterium R. palustris | ||||||
Components | Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1 | ||||||
Keywords | SIGNALING PROTEIN / PAS fold / photoreceptor / response regulator RPA3017 / TRANSFERASE | ||||||
Function / homology | Function and homology information detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris CGA009 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.395 Å | ||||||
Authors | Yang, X. / Stojkovic, E. / Ozarowski, W. / Kuk, J. / Davydova, E. / Moffat, K. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Light Signaling Mechanism of Two Tandem Bacteriophytochromes. Authors: Yang, X. / Stojkovic, E.A. / Ozarowski, W.B. / Kuk, J. / Davydova, E. / Moffat, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r6l.cif.gz | 379.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r6l.ent.gz | 316.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r6l_validation.pdf.gz | 997.8 KB | Display | wwPDB validaton report |
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Full document | 4r6l_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4r6l_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 4r6l_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6l ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6l | HTTPS FTP |
-Related structure data
Related structure data | 4r70C 4s21C 2oolS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56814.555 Da / Num. of mol.: 2 / Fragment: photosensory core module, UNP residues 1-506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic) Strain: CGA009 / Gene: phyB1, RPA3015 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N5G3 #2: Chemical | |
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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: 3.81 Å3/Da / Density % sol: 67.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10mg/ml protein, 12% polyacrylic acid, 0.1M MgCl2, 0.1M Hepes (pH7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 8, 2009 |
Radiation | Monochromator: diamond laue monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.306→50 Å / Num. obs: 22049 / % possible obs: 62 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OOL Resolution: 3.395→49.021 Å / SU ML: 0.66 / σ(F): 1.34 / Phase error: 41.64 / Stereochemistry target values: ML Details: Author states that issues with the main chain geometry and the high B-factors are largely due to the poor resolution.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.395→49.021 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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