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Yorodumi- PDB-4rvy: Serial Time resolved crystallography of Photosystem II using a fe... -
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-Basic information
Entry | Database: PDB / ID: 4rvy | ||||||||||||
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Title | Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3) | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Photosystem II / Time resolved / Free electron laser / ELECTRON TRANSPORT / Membrane | ||||||||||||
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 / 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: 5.5 Å | ||||||||||||
Authors | Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N. / Rendek, K.N. / Hunter, M. / Shoeman, R.L. / White, T.A. / Wang, D. ...Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N. / Rendek, K.N. / Hunter, M. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.-H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A. / Deponte, D. / Kirian, R. / Bari, S. / Bergkamp, J.J. / Beyerlein, K. / Bogan, M.J. / Caleman, C. / Chao, T.-C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C.H. / Fromme, P. | ||||||||||||
Citation | Journal: Nature / Year: 2014 Title: Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Authors: Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N.A. / Rendek, K.N. / Hunter, M.S. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. ...Authors: Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N.A. / Rendek, K.N. / Hunter, M.S. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A.L. / Deponte, D. / Kirian, R.A. / Bari, S. / Bergkamp, J.J. / Beyerlein, K.R. / Bogan, M.J. / Caleman, C. / Chao, T.C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C. / Fromme, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rvy.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4rvy.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4rvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rvy_validation.pdf.gz | 18.1 MB | Display | wwPDB validaton report |
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Full document | 4rvy_full_validation.pdf.gz | 18.7 MB | Display | |
Data in XML | 4rvy_validation.xml.gz | 255.4 KB | Display | |
Data in CIF | 4rvy_validation.cif.gz | 304.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rvy ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rvy | HTTPS FTP |
-Related structure data
Related structure data | 4pbuC 3arc 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 ... , 16 types, 32 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuXxYyZz
#1: Protein | Mass: 37029.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444, photosystem II #2: Protein | Mass: 55939.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (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 (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8 #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II #7: Protein | Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (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 (bacteria) / Strain: BP-1 / References: UniProt: P59087 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (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 (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 3807.517 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7 #13: Protein | Mass: 26523.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431 #14: Protein/peptide | Mass: 3620.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0 #15: Protein | Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5 #17: Protein/peptide | Mass: 4077.873 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6 #18: Protein/peptide | Mass: 3098.921 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1 #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9321.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 3868.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Protein / Sugars , 2 types, 12 molecules Vv
#16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386 #31: Sugar | ChemComp-DGD / |
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-Non-polymers , 14 types, 156 molecules
#20: Chemical | #21: Chemical | #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-PHO / #24: Chemical | ChemComp-BCR / #25: Chemical | ChemComp-SQD / #26: Chemical | ChemComp-CL / #27: Chemical | #28: Chemical | ChemComp-PL9 / #29: Chemical | ChemComp-LMG / #30: Chemical | ChemComp-CA / #32: Chemical | ChemComp-LHG / #33: Chemical | ChemComp-HEM / #34: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 18772 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70.02 % |
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Crystal grow | Temperature: 283 K / Method: free interface diffusion / pH: 7 Details: 100 mM Pipes pH 7.0, 5 mM CaCl2, 10 mM tocopherol, and 10-17% PEG 2000 , Free interface diffusion, temperature 283K, temperature 283.0K |
-Data collection
Diffraction | Mean temperature: 283 K | |||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 2.05 Å | |||||||||||||||||||||||||||||||||||||||
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jan 25, 2012 | |||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 2.05 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 5.5→102.295 Å / Num. all: 33992 / Num. obs: 32066 / % possible obs: 99.88 % | |||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ARC 3arc Resolution: 5.5→102.295 Å / σ(F): 1.35
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Refinement step | Cycle: LAST / Resolution: 5.5→102.295 Å
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LS refinement shell |
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