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Yorodumi- PDB-5mg1: Structure of the photosensory module of Deinococcus phytochrome b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mg1 | ||||||
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Title | Structure of the photosensory module of Deinococcus phytochrome by serial femtosecond X-ray crystallography | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / Photosensory module / phytochrome / biliverdin / photoreceptor | ||||||
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 / molecular replacement / Resolution: 3.3 Å | ||||||
Authors | Burgie, E.S. / Fuller, F.D. / Gul, S. / Young, I.D. / Brewster, A.S. / Clinger, J. / Andi, B. / Stan, C. / Allaire, M. / Nelsen, S. ...Burgie, E.S. / Fuller, F.D. / Gul, S. / Young, I.D. / Brewster, A.S. / Clinger, J. / Andi, B. / Stan, C. / Allaire, M. / Nelsen, S. / Alonso-Mori, R. / Phillips Jr., G.N. / Sauter, N.K. / Kern, J. / Yachandra, V.K. / Yano, J. / Vierstra, R.D. / Orville, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat. Methods / Year: 2017 Title: Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. ...Authors: Fuller, F.D. / Gul, S. / Chatterjee, R. / Burgie, E.S. / Young, I.D. / Lebrette, H. / Srinivas, V. / Brewster, A.S. / Michels-Clark, T. / Clinger, J.A. / Andi, B. / Ibrahim, M. / Pastor, E. / de Lichtenberg, C. / Hussein, R. / Pollock, C.J. / Zhang, M. / Stan, C.A. / Kroll, T. / Fransson, T. / Weninger, C. / Kubin, M. / Aller, P. / Lassalle, L. / Brauer, P. / Miller, M.D. / Amin, M. / Koroidov, S. / Roessler, C.G. / Allaire, M. / Sierra, R.G. / Docker, P.T. / Glownia, J.M. / Nelson, S. / Koglin, J.E. / Zhu, D. / Chollet, M. / Song, S. / Lemke, H. / Liang, M. / Sokaras, D. / Alonso-Mori, R. / Zouni, A. / Messinger, J. / Bergmann, U. / Boal, A.K. / Bollinger, J.M. / Krebs, C. / Hogbom, M. / Phillips, G.N. / Vierstra, R.D. / Sauter, N.K. / Orville, A.M. / Kern, J. / Yachandra, V.K. / Yano, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mg1.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mg1.ent.gz | 166.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mg1_validation.pdf.gz | 746.3 KB | Display | wwPDB validaton report |
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Full document | 5mg1_full_validation.pdf.gz | 748.6 KB | Display | |
Data in XML | 5mg1_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 5mg1_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mg1 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mg1 | HTTPS FTP |
-Related structure data
Related structure data | 5mg0C 2o9cS 4q0jS 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: 56694.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: bphP, DR_A0050 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase |
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#2: Chemical | ChemComp-LBV / |
#3: 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: 4.43 Å3/Da / Density % sol: 72.23 % / Description: 100 micron needles |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.5 Details: PEG 3350, Tacsimate pH 6.0, Tacsimate pH 7.0, ethylene glycol, PIPES-NaOH pH 6.5 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX170-HS / Detector: CCD / Date: Oct 31, 2015 / Details: Compound refractive lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.305 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→131.376 Å / Num. obs: 15996 / % possible obs: 99.86 % / Redundancy: 39.16 % / CC1/2: 0.863 / Net I/σ(I): 29.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PAS-GAF from PDB 2O9C, and PHY domain from 4Q0J Resolution: 3.3→37.894 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 203.52 Å2 / Biso mean: 91.6934 Å2 / Biso min: 38.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→37.894 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -14.1022 Å / Origin y: 65.3452 Å / Origin z: 8.3921 Å
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Refinement TLS group | Selection details: chain 'A' and (resid 6 through 550 ) |