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- PDB-4pj0: Structure of T.elongatus Photosystem II, rows of dimers crystal p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pj0 | |||||||||
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Title | Structure of T.elongatus Photosystem II, rows of dimers crystal packing | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hellmich, J. / Bommer, M. / Burkhardt, A. / Ibrahim, M. / Kern, J. / Meents, A. / Mueh, F. / Dobbek, H. / Zouni, A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 25.5 MB | Display | ![]() |
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Full document | ![]() | 25.8 MB | Display | |
Data in XML | ![]() | 211.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3arc S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() Strain: BP-1 / References: UniProt: P0A444, ![]() #2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q9F1M3, UniProt: Q8DIQ1*PLUS, ![]() #16: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A386, ![]() |
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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) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8CM25, ![]() #7: Protein | ![]() Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN8, ![]() #12: Protein/peptide | ![]() Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: P0A431, ![]() #14: Protein/peptide | ![]() Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIQ0, ![]() #15: Protein | ![]() Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1L5, ![]() #17: Protein/peptide | ![]() Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJI1, ![]() #18: Protein/peptide | ![]() Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DHJ2, ![]() #20: Protein/peptide | ![]() Mass: 4590.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DKM3, ![]() |
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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) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN9, ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1690) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() 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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