+Open data
-Basic information
Entry | Database: PDB / ID: 5k5b | ||||||
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Title | Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / Kinase Photosensor Transferase Phytochrome | ||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Takala, H. / Edlund, P. / Claesson, E. / Ihalainen, J.A. / Westenhoff, S. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. Authors: Edlund, P. / Takala, H. / Claesson, E. / Henry, L. / Dods, R. / Lehtivuori, H. / Panman, M. / Pande, K. / White, T. / Nakane, T. / Berntsson, O. / Gustavsson, E. / Bath, P. / Modi, V. / Roy- ...Authors: Edlund, P. / Takala, H. / Claesson, E. / Henry, L. / Dods, R. / Lehtivuori, H. / Panman, M. / Pande, K. / White, T. / Nakane, T. / Berntsson, O. / Gustavsson, E. / Bath, P. / Modi, V. / Roy-Chowdhury, S. / Zook, J. / Berntsen, P. / Pandey, S. / Poudyal, I. / Tenboer, J. / Kupitz, C. / Barty, A. / Fromme, P. / Koralek, J.D. / Tanaka, T. / Spence, J. / Liang, M. / Hunter, M.S. / Boutet, S. / Nango, E. / Moffat, K. / Groenhof, G. / Ihalainen, J. / Stojkovic, E.A. / Schmidt, M. / Westenhoff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k5b.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k5b.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k5b_validation.pdf.gz | 790.8 KB | Display | wwPDB validaton report |
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Full document | 5k5b_full_validation.pdf.gz | 792.8 KB | Display | |
Data in XML | 5k5b_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5k5b_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/5k5b ftp://data.pdbj.org/pub/pdb/validation_reports/k5/5k5b | HTTPS FTP |
-Related structure data
Related structure data | 5l8mC 5lbrC 4q0hS 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: 37229.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: bphP, DR_A0050 / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZA4, histidine kinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MPD / ( | #4: Chemical | ChemComp-LBV / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.95 Details: sodium acetate, PEG 400, DTT, 2-methyl-2, 4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.972957 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→46.97 Å / Num. obs: 75872 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.36 % / Biso Wilson estimate: 25.092 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q0H Resolution: 1.35→39.37 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.483 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0479 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.41 Å2 / Biso mean: 25.474 Å2 / Biso min: 11.78 Å2
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Refinement step | Cycle: final / Resolution: 1.35→39.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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