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Yorodumi- PDB-7rf2: RT XFEL structure of dark-stable state of Photosystem II (0F, S1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rf2 | |||||||||||||||||||||||||||||||||||||||
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Title | RT XFEL structure of dark-stable state of Photosystem II (0F, S1 rich) at 2.08 Angstrom | |||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Membrane protein / Photosystem II | |||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M.D. / Bogacz, I. / Kim, I.-S. / Cheah, M.H. ...Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M.D. / Bogacz, I. / Kim, I.-S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, C.C. / Young, I.D. / Carbajo, S. / Fuller, F.D. / Alonso-Mori, R. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bolotovski, R. / Mendez, D. / Holton, J.M. / Moriarty, N.W. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Dobbek, H. / Messinger, J. / Zouni, A. / Kern, J. / Yachandra, V.K. / Yano, J. | |||||||||||||||||||||||||||||||||||||||
Funding support | United States, Germany, Sweden, 12items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition. Authors: Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M. / Bogacz, I. / Kim, I.S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, ...Authors: Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M. / Bogacz, I. / Kim, I.S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, C.C. / Young, I.D. / Carbajo, S. / Fuller, F.D. / Alonso-Mori, R. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bolotovsky, R. / Mendez, D. / Holton, J.M. / Moriarty, N.W. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Dobbek, H. / Messinger, J. / Zouni, A. / 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 | 7rf2.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7rf2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7rf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/7rf2 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/7rf2 | HTTPS FTP |
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-Related structure data
Related structure data | 7rf1C 7rf3C 7rf4C 7rf5C 7rf6C 7rf7C 7rf8C 6dheS 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
-Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A444, photosystem II #2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIQ1 #3: Protein | Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIF8 #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8CM25, photosystem II #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DJZ6 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P59087 #10: Protein/peptide | Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DHA7 #13: Protein | Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A431 #14: Protein/peptide | Mass: 4590.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DKM3 #15: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIQ0 #16: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1L5 #18: Protein/peptide | Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1R6 #19: Protein/peptide | Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DJI1 #20: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DHJ2 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Protein / Sugars , 2 types, 12 molecules Vv
#17: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A386 #30: Sugar | ChemComp-DGD / |
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-Non-polymers , 15 types, 2179 molecules
#21: Chemical | #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-PHO / #24: Chemical | ChemComp-BCR / #25: Chemical | ChemComp-CL / #26: Chemical | ChemComp-PL9 / #27: Chemical | ChemComp-LMG / #28: Chemical | ChemComp-SQD / #29: Chemical | ChemComp-LHG / #31: Chemical | #32: Chemical | ChemComp-STE / #33: Chemical | #34: Chemical | #35: Chemical | #36: Water | ChemComp-HOH / | |
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-Details
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: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000 |
-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: MFX / Wavelength: 1.30183 Å |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Nov 27, 2018 / Frequency: 20 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.30183 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→33.64 Å / Num. obs: 474828 / % possible obs: 99.77 % / Redundancy: 89.1 % / Biso Wilson estimate: 34.44 Å2 / CC1/2: 0.98 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.08→2.12 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 23014 / CC1/2: 0.054 / % possible all: 97.48 |
Serial crystallography measurement | Collimation: Compound refractive lenses / Focal spot size: 9 µm2 / Pulse duration: 40 fsec. / Pulse energy: 3000 µJ / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 20 Hz |
Serial crystallography sample delivery | Description: Drop-on-Tape / Method: injection |
Serial crystallography sample delivery injection | Description: Acoustic Droplet Ejection / Flow rate: 4 µL/min / Power by: acoustic wave |
Serial crystallography data reduction | Lattices indexed: 11734 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DHE Resolution: 2.08→33.64 Å / SU ML: 0.348 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9399 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→33.64 Å
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Refine LS restraints |
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LS refinement shell |
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