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Yorodumi- PDB-6t3l: PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t3l | |||||||||||||||
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Title | PAS-GAF fragment from Deinococcus radiodurans phytochrome in dark state | |||||||||||||||
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 / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å | |||||||||||||||
Authors | Claesson, E. / Takala, H. / Yuan Wahlgren, W. / Pandey, S. / Schmidt, M. / Westenhoff, S. | |||||||||||||||
Funding support | Sweden, Japan, Finland, 4items
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Citation | Journal: Elife / Year: 2020 Title: The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser. Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / ...Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / Cellini, A. / Morozov, D. / Maj, M. / Kurttila, M. / Bosman, R. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Iwata, S. / Owada, S. / Moffat, K. / Groenhof, G. / A Stojkovic, E. / A Ihalainen, J. / 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 | 6t3l.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t3l.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 6t3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t3l_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6t3l_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6t3l_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 6t3l_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/6t3l ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t3l | HTTPS FTP |
-Related structure data
Related structure data | 6t3uC 5k5bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1607859 / 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.: 2 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 BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 4.95 Details: 60 mM Sodium Acetate, 3.3% PEG400, 1 mM DTT, 30% 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: 1.7712 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Oct 12, 2018 |
Radiation | Monochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→45.87 Å / Num. obs: 52060 / % possible obs: 100 % / Redundancy: 461.35 % / CC1/2: 0.99 / R split: 0.0579 / Net I/σ(I): 9.21 |
Reflection shell | Resolution: 2.07→2.1 Å / Redundancy: 65.9 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 2052 / CC1/2: 0.33 / R split: 1.2005 / % possible all: 100 |
Serial crystallography sample delivery | Description: grease jet / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Superlube |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K5B Resolution: 2.07→45.82 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.02 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1698 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.145 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 184.06 Å2 / Biso mean: 76.469 Å2 / Biso min: 50.43 Å2
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Refinement step | Cycle: final / Resolution: 2.07→45.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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