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Yorodumi- PDB-5e7c: Macromolecular diffractive imaging using imperfect crystals - Bra... -
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-Basic information
Entry | Database: PDB / ID: 5e7c | ||||||||||||||||||||||||
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Title | Macromolecular diffractive imaging using imperfect crystals - Bragg data | ||||||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem II / XFEL / SFX | ||||||||||||||||||||||||
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: 4.5 Å | ||||||||||||||||||||||||
Authors | Ayyer, K. / Yefanov, O. / Oberthuer, D. / Roy-Chowdhury, S. / Galli, L. / Mariani, V. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. ...Ayyer, K. / Yefanov, O. / Oberthuer, D. / Roy-Chowdhury, S. / Galli, L. / Mariani, V. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Schaffner, A. / Doerner, K. / James, D. / Kupitz, C. / Metz, M. / Nelson, G. / Xavier, P.L. / Beyerlein, K.R. / Schmidt, M. / Sarrou, I. / Spence, J.C.H. / Weierstall, U. / White, T.A. / Yang, J.-H. / Zhao, Y. / Liang, M. / Aquila, A. / Hunter, M.S. / Robinson, J.S. / Koglin, J.E. / Boutet, S. / Fromme, P. / Barty, A. / Chapman, H.N. | ||||||||||||||||||||||||
Funding support | Germany, United States, 7items
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Citation | Journal: Nature / Year: 2016 Title: Macromolecular diffractive imaging using imperfect crystals. Authors: Ayyer, K. / Yefanov, O.M. / Oberthur, D. / Roy-Chowdhury, S. / Galli, L. / Mariani, V. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Schaffer, A. / Dorner, K. / James, D. / Kupitz, C. / ...Authors: Ayyer, K. / Yefanov, O.M. / Oberthur, D. / Roy-Chowdhury, S. / Galli, L. / Mariani, V. / Basu, S. / Coe, J. / Conrad, C.E. / Fromme, R. / Schaffer, A. / Dorner, K. / James, D. / Kupitz, C. / Metz, M. / Nelson, G. / Xavier, P.L. / Beyerlein, K.R. / Schmidt, M. / Sarrou, I. / Spence, J.C. / Weierstall, U. / White, T.A. / Yang, J.H. / Zhao, Y. / Liang, M. / Aquila, A. / Hunter, M.S. / Robinson, J.S. / Koglin, J.E. / Boutet, S. / Fromme, P. / Barty, A. / Chapman, H.N. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e7c.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5e7c.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5e7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e7c_validation.pdf.gz | 19.4 MB | Display | wwPDB validaton report |
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Full document | 5e7c_full_validation.pdf.gz | 20.2 MB | Display | |
Data in XML | 5e7c_validation.xml.gz | 280.4 KB | Display | |
Data in CIF | 5e7c_validation.cif.gz | 331.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e7c ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e7c | HTTPS FTP |
-Related structure data
Related structure data | 5e79C 3arc S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1341415 / 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
-Photosystem II ... , 16 types, 32 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXxZz
#1: Protein | Mass: 37029.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Photosystem Q(B) protein 1 Source: (natural) Thermosynechococcus elongatus (strain BP-1) (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 (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIQ1 #3: Protein | Mass: 49207.250 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: 38404.949 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: 7227.559 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: 4410.245 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: 3843.517 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: 4101.911 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: 3807.517 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: 26523.578 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: 3620.369 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 #15: Protein | Mass: 10966.317 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 #17: Protein/peptide | Mass: 3098.921 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 #18: Protein/peptide | Mass: 4077.873 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 | 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: 9321.515 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: 3868.611 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
#16: Protein | Mass: 15148.255 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: P0A386 #32: Sugar | ChemComp-DGD / |
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-Non-polymers , 14 types, 154 molecules
#20: Chemical | #21: Chemical | ChemComp-CL / #22: Chemical | #23: Chemical | ChemComp-CLA / #24: Chemical | ChemComp-PHO / #25: Chemical | ChemComp-BCR / #26: Chemical | ChemComp-PL9 / #27: Chemical | ChemComp-SQD / #28: Chemical | ChemComp-LMG / #29: Chemical | #30: Chemical | ChemComp-CA / #31: 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 283 K / Method: liquid diffusion / pH: 7 Details: 100 mM Pipes pH 7.0, 5 mM CaCl2, 10 mM tocopherol, and 10-17% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.308 Å |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.308 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→30 Å / Num. obs: 55609 / % possible obs: 99.9 % / Redundancy: 1 % / CC1/2: 0.99 / R split: 0.1148 / Net I/σ(I): 5.01 |
Reflection shell | Resolution: 4.5→4.62 Å / Mean I/σ(I) obs: 1.49 / CC1/2: 0.94 / R split: 0.4616 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: modified version of 3ARC 3arc Resolution: 4.5→29.925 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.5→29.925 Å
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Refine LS restraints |
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LS refinement shell |
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