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Yorodumi- PDB-4pj0: Structure of T.elongatus Photosystem II, rows of dimers crystal p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pj0 | ||||||||||||
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Title | Structure of T.elongatus Photosystem II, rows of dimers crystal packing | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / Membrane Protein / Photosystem II / C12E8 | ||||||||||||
Function / homology | Function and homology information thylakoid membrane / 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 ...thylakoid membrane / 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 / membrane => GO:0016020 / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.437 Å | ||||||||||||
Authors | Hellmich, J. / Bommer, M. / Burkhardt, A. / Ibrahim, M. / Kern, J. / Meents, A. / Mueh, F. / Dobbek, H. / Zouni, A. | ||||||||||||
Citation | Journal: Structure / Year: 2014 Title: Native-like Photosystem II Superstructure at 2.44 angstrom Resolution through Detergent Extraction from the Protein Crystal. Authors: Hellmich, J. / Bommer, M. / Burkhardt, A. / Ibrahim, M. / Kern, J. / Meents, A. / Muh, F. / Dobbek, H. / Zouni, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pj0.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4pj0.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4pj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/4pj0 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/4pj0 | HTTPS FTP |
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-Related structure data
Related structure data | 3arc S: Starting model for refinement |
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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
-Protein , 3 types, 6 molecules AaBbVv
#1: Protein | Mass: 38265.625 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: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) References: UniProt: Q9F1M3, UniProt: Q8DIQ1*PLUS, photosystem II #16: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386, photosystem II |
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-Photosystem II ... , 15 types, 30 molecules CcDdHhIiJjKkLlMmOoTtUuYyXxZzRr
#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, photosystem II #4: Protein | Mass: 39388.156 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: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43, photosystem II #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, photosystem II #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, photosystem II #10: Protein/peptide | Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9, photosystem II #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, photosystem II #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7, photosystem II #13: Protein | Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431, photosystem II #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0, photosystem II #15: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5, photosystem II #17: Protein/peptide | Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1, photosystem II #18: Protein/peptide | Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6, photosystem II #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, photosystem II #20: Protein/peptide | Mass: 4590.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DKM3, photosystem II |
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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 (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0, photosystem II #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9, photosystem II |
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-Sugars , 1 types, 8 molecules
#33: Sugar | ChemComp-DGD / |
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-Non-polymers , 16 types, 487 molecules
#21: Chemical | #22: Chemical | #23: Chemical | ChemComp-LMG / #24: Chemical | ChemComp-CL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-BCR / #27: Chemical | ChemComp-PL9 / #28: Chemical | ChemComp-SQD / #29: Chemical | ChemComp-LHG / #30: Chemical | ChemComp-SO4 / #31: Chemical | #32: Chemical | ChemComp-UNL / Num. of mol.: 29 / Source method: obtained synthetically #34: Chemical | ChemComp-PHO / #35: Chemical | #36: Chemical | #37: Water | ChemComp-HOH / | |
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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: 3.04 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: Batch crystallisation: 2 mM Chl a equivalent of PSIIcc mixed 1:1 with: 0.1 M TRIS (pH 7.5), 0.1 M (NH4)2SO4, 15 - 18 % PEG 5000 MME, post-crystallisation dehydration |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Type: OTHER / Wavelength: 1.196 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2013 |
Radiation | Monochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.196 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→49.12 Å / Num. obs: 282213 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.44→2.524 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6979 / Mean I/σ(I) obs: 1.93 / % possible all: 89.5 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1690) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ARC 3arc Resolution: 2.437→49.123 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / 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: 2.437→49.123 Å
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Refine LS restraints |
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LS refinement shell |
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