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Yorodumi- PDB-5lbr: Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp coll... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lbr | ||||||
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Title | Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / Kinase / Photosensor / 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 / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Edlund, P. / Claesson, E. / Nakane, T. / Takala, H. / Dods, R. / Schmidt, M. / 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 | 5lbr.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lbr.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbr ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbr | HTTPS FTP |
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-Related structure data
Related structure data | 5k5bC 5l8mC 4q0hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1329634 / Data set type: diffraction image 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 | ChemComp-LBV / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.57 Å3/Da / Density % sol: 52.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.95 / Details: Sodium Acetate, Peg400, 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.987 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 1, 2015 |
Radiation | Monochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→71.54 Å / Num. obs: 18818 / % possible obs: 100 % / Redundancy: 81.2 % / CC1/2: 0.976 / R split: 0.119 / Net I/σ(I): 5.62 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 0.68 / R split: 0.677 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q0H Resolution: 2.2→71.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.961 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 50.258 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→71.54 Å
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