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Open data
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Basic information
Entry | Database: PDB / ID: 5b5e | |||||||||
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Title | Crystal structure analysis of Photosystem II complex | |||||||||
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![]() | ELECTRON TRANSPORT / PHOTOSYNTHESIS / psii / photosystem / membrane complex / transmembrane alpha-helix / oxygen evolving / water splitting / iron binding / calcium binding / manganese binding / chloride binding / formylation / hydroxylation / thylakoid membrane | |||||||||
Function / homology | ![]() photosystem II assembly / photosystem II oxygen evolving complex / 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 assembly / photosystem II oxygen evolving complex / 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Tanaka, A. / Fukushima, Y. / Kamiya, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II Authors: Tanaka, A. / Fukushima, Y. / Kamiya, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 37.2 MB | Display | ![]() |
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Full document | ![]() | 37.7 MB | Display | |
Data in XML | ![]() | 319 KB | Display | |
Data in CIF | ![]() | 415.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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) ![]() #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: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 7227.559 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 / Details: FME 1 (Modified residue: N-FORMYLMETHIONINE) / 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: 3981.673 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 / Details: FME 1 (Modified residue: N-FORMYLMETHIONINE) / 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: 6766.187 Da / Num. of mol.: 2 / 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, 46 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)
#30: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-HTG / #36: Sugar | ChemComp-DGD / |
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-Non-polymers , 19 types, 3944 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/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/LMG.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/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/LMG.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)
#20: Chemical | #21: Chemical | #22: Chemical | ChemComp-CL / #23: Chemical | ChemComp-CLA / #24: Chemical | ChemComp-PHO / #25: Chemical | ChemComp-BCR / #26: Chemical | ChemComp-SQD / #27: Chemical | ChemComp-PL9 / #28: Chemical | ChemComp-LHG / #29: Chemical | ChemComp-UNL / Num. of mol.: 53 / Source method: obtained synthetically #31: Chemical | ChemComp-DMS / #32: Chemical | #33: Chemical | ChemComp-CA / #34: Chemical | ChemComp-LMG / #37: Chemical | #38: Chemical | #39: Chemical | #40: Chemical | #41: Water | ChemComp-HOH / | |
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-Details
Sequence details | ABOUT PRO A(a) 279, LEU K(k) 33, TRP K(k) 39 AND LEU M(m) 8, THE AUTHOR CONFIRMED BY ELECTRON ...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. SEQUENCE DIFFERENCE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.27 % |
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Crystal grow | Temperature: 285 K / Method: microbatch / pH: 6.1 / Details: Mes,NaCl,CaCl2,MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→49 Å / Num. obs: 649016 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.2 |
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Processing
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Refinement | Resolution: 1.87→48.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.165 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→48.98 Å
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