+Open data
-Basic information
Entry | Database: PDB / ID: 8gn0 | ||||||
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Title | Crystal structure of DCBQ-bound photosystem II complex | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem / electron transfer / electron acceptor / Quinone | ||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 / photosynthetic electron transport in photosystem II / extrinsic component of membrane / 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermostichus vulcanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Kamada, S. / Nakajima, Y. / Shen, J.-R. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. Authors: Kamada, S. / Nakajima, Y. / Shen, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gn0.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8gn0.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 8gn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/8gn0 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/8gn0 | HTTPS FTP |
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-Related structure data
Related structure data | 8gn1C 8gn2C 3wu2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 38235.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P51765, photosystem II #2: Protein | Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR1 #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR7 #4: Protein | Mass: 38419.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II #7: Protein | Mass: 7057.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P19052 #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12240 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: Q7DGD4 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P19054 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12241 #12: Protein/peptide | Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12312 #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR2 #14: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12313 #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P56152 #17: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR3 #18: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR4 #19: Protein | Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: D0VWR5 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9449.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12238 #6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P12239 |
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-Protein , 1 types, 2 molecules Vv
#16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermostichus vulcanus (bacteria) / References: UniProt: P0A387 |
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-Sugars , 3 types, 49 molecules
#28: Sugar | ChemComp-LMT / #36: Sugar | ChemComp-HTG / #37: Sugar | ChemComp-DGD / |
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+Non-polymers , 21 types, 2811 molecules
-Details
Has ligand of interest | Y |
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Sequence details | SEQUENCE ABOUT PRO A(A) 279, LEU K(K) 33, TRP K(K) 39 AND LEU M(M) 8, THE AUTHOR CONFIRMED BY ...SEQUENCE ABOUT PRO A(A) 279, LEU K(K) 33, TRP K(K) 39 AND LEU M(M) 8, THE AUTHOR CONFIRMED BY ELECTRON DENSITY MAP. THESE RESIDUES OF CHAIN C(C) ARE BASED ON THE DATABASE SEQUENCE FROM THERMOSYNE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % |
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Crystal grow | Temperature: 285 K / Method: microbatch / pH: 6.1 Details: 5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM MES buffer, pH 6.1, MICRO-BATCH METHOD UNDER OIL, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 13, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 428716 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.472 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 42587 / CC1/2: 0.724 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3wu2 Resolution: 2.15→49 Å / SU ML: 0.2289 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2185 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: 64.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.8309645045 Å / Origin y: -13.137060021 Å / Origin z: 25.8681813341 Å
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Refinement TLS group | Selection details: all |