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Yorodumi- PDB-5l8m: Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp coll... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l8m | ||||||
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Title | Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS | ||||||
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: 2.1 Å | ||||||
Authors | Claesson, E. / Takala, H. / Edlund, P. / Henry, L. / 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 | 5l8m.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l8m.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/5l8m ftp://data.pdbj.org/pub/pdb/validation_reports/l8/5l8m | HTTPS FTP |
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-Related structure data
Related structure data | 5k5bC 5lbrC 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) 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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 283 K / Method: batch mode / pH: 4.95 Details: sodium acetate, DTT, 2-methyl-2,4-pentandiol, PEG400 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jan 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.2 Å / Num. obs: 20853 / % possible obs: 99.97 % / Redundancy: 819 % / CC1/2: 0.98 / R split: 0.0919 / Net I/σ(I): 7.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q0H Resolution: 2.1→38.2 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.076 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.174 / 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: 42.92 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→38.2 Å
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Refine LS restraints |
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