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Open data
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Basic information
Entry | Database: PDB / ID: 8gn1 | ||||||
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Title | Crystal structure of DBBQ-bound photosystem II complex | ||||||
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![]() | PHOTOSYNTHESIS / Photosystem / electron transfer / electron acceptor / Quinone | ||||||
Function / homology | ![]() 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 / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamada, S. / Nakajima, Y. / Shen, J.-R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | 2.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gn0C ![]() 8gn2C ![]() 3wu2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Photosystem II ... , 17 types, 33 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...
#1: Protein | Mass: 38235.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 38419.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7057.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein/peptide | Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein/peptide | | Mass: 4590.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() #6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() |
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-Sugars , 3 types, 50 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/HTG.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/HTG.gif)
![](data/chem/img/DGD.gif)
#29: Sugar | ChemComp-LMT / #36: Sugar | ChemComp-HTG / #38: Sugar | ChemComp-DGD / |
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+Non-polymers , 21 types, 2919 molecules ![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/K2I.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/K2I.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
-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: ![]() |
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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: ![]() ![]() ![]() |
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: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 460342 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 43.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 45180 / CC1/2: 0.653 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3wu2 Resolution: 2.1→49.02 Å / SU ML: 0.2416 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7943 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: 59.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.02 Å
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Refine LS restraints |
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LS refinement shell |
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