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Yorodumi- PDB-6w1t: RT XFEL structure of Photosystem II 250 microseconds after the se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w1t | |||||||||||||||||||||||||||||||||||||||||||||
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Title | RT XFEL structure of Photosystem II 250 microseconds after the second illumination at 2.01 Angstrom resolution | |||||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / water oxidation / membrane protein / light harvesting / electron transfer | |||||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / manganese ion binding / protein stabilization / electron transfer activity / 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: 2.01 Å | |||||||||||||||||||||||||||||||||||||||||||||
Authors | Ibrahim, M. / Fransson, T. / Chatterjee, R. / Cheah, M.H. / Hussein, R. / Lassalle, L. / Sutherlin, K.D. / Young, I.D. / Fuller, F.D. / Gul, S. ...Ibrahim, M. / Fransson, T. / Chatterjee, R. / Cheah, M.H. / Hussein, R. / Lassalle, L. / Sutherlin, K.D. / Young, I.D. / Fuller, F.D. / Gul, S. / Kim, I.-S. / Simon, P.S. / de Lichtenberg, C. / Chernev, P. / Bogacz, I. / Pham, C. / Orville, A.M. / Saichek, N. / Northen, T.R. / Batyuk, A. / Carbajo, S. / Alonso-Mori, R. / Tono, K. / Owada, S. / Bhowmick, A. / Bolotovski, R. / Mendez, D. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Brewster, A.S. / Adams, P.D. / Sauter, N.K. / Bergmann, U. / Zouni, A. / Messinger, J. / Kern, J. / Yachandra, V.K. / Yano, J. | |||||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, Germany, Sweden, United Kingdom, 14items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Untangling the sequence of events during the S2→ S3transition in photosystem II and implications for the water oxidation mechanism. Authors: Ibrahim, M. / Fransson, T. / Chatterjee, R. / Cheah, M.H. / Hussein, R. / Lassalle, L. / Sutherlin, K.D. / Young, I.D. / Fuller, F.D. / Gul, S. / Kim, I.S. / Simon, P.S. / de Lichtenberg, C. ...Authors: Ibrahim, M. / Fransson, T. / Chatterjee, R. / Cheah, M.H. / Hussein, R. / Lassalle, L. / Sutherlin, K.D. / Young, I.D. / Fuller, F.D. / Gul, S. / Kim, I.S. / Simon, P.S. / de Lichtenberg, C. / Chernev, P. / Bogacz, I. / Pham, C.C. / Orville, A.M. / Saichek, N. / Northen, T. / Batyuk, A. / Carbajo, S. / Alonso-Mori, R. / Tono, K. / Owada, S. / Bhowmick, A. / Bolotovsky, R. / Mendez, D. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Brewster, A.S. / Adams, P.D. / Sauter, N.K. / Bergmann, U. / Zouni, A. / Messinger, J. / 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 | 6w1t.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6w1t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6w1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w1t_validation.pdf.gz | 37.1 MB | Display | wwPDB validaton report |
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Full document | 6w1t_full_validation.pdf.gz | 37.3 MB | Display | |
Data in XML | 6w1t_validation.xml.gz | 274.1 KB | Display | |
Data in CIF | 6w1t_validation.cif.gz | 353.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1t ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1t | HTTPS FTP |
-Related structure data
Related structure data | 6w1oC 6w1pC 6w1qC 6w1rC 6w1uC 6w1vC 6dheS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 56227.953 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: 4459.453 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: 3648.379 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, 11 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, 2279 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-LHG / #29: Chemical | ChemComp-SQD / #31: Chemical | #32: Chemical | #33: Chemical | ChemComp-STE / #34: Chemical | #35: Chemical | ChemComp-HEC / #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: 3.18 Å3/Da / Density % sol: 61.27 % |
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Crystal grow | Temperature: 298 K / Method: batch mode Details: 0.1 M MES, pH 6.5, 0.1 M ammonium chloride, 35% w/v PEG5000 |
-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: 1.3027 Å |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Nov 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3027 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→33.59 Å / Num. obs: 535670 / % possible obs: 99.78 % / Redundancy: 71.1 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.977 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.01→2.03 Å / Num. unique obs: 25929 / CC1/2: 0.051 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6DHE Resolution: 2.01→33.59 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.1176 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: 39.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→33.59 Å
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Refine LS restraints |
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LS refinement shell |
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