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- PDB-8ir6: XFEL structure of cyanobacterial photosystem II following one fla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ir6 | |||||||||
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Title | XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 20-nanosecond delay | |||||||||
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![]() | PHOTOSYNTHESIS / PSII / photosystem II / XFEL | |||||||||
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 / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, H. / Suga, M. / Shen, J.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions. Authors: Li, H. / Nakajima, Y. / Nango, E. / Owada, S. / Yamada, D. / Hashimoto, K. / Luo, F. / Tanaka, R. / Akita, F. / Kato, K. / Kang, J. / Saitoh, Y. / Kishi, S. / Yu, H. / Matsubara, N. / Fujii, ...Authors: Li, H. / Nakajima, Y. / Nango, E. / Owada, S. / Yamada, D. / Hashimoto, K. / Luo, F. / Tanaka, R. / Akita, F. / Kato, K. / Kang, J. / Saitoh, Y. / Kishi, S. / Yu, H. / Matsubara, N. / Fujii, H. / Sugahara, M. / Suzuki, M. / Masuda, T. / Kimura, T. / Thao, T.N. / Yonekura, S. / Yu, L.J. / Tosha, T. / Tono, K. / Joti, Y. / Hatsui, T. / Yabashi, M. / Kubo, M. / Iwata, S. / Isobe, H. / Yamaguchi, K. / Suga, M. / 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 | ![]() | 2.9 MB | Display | ![]() |
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PDB format | ![]() | 2.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 44.5 MB | Display | ![]() |
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Full document | ![]() | 45.5 MB | Display | |
Data in XML | ![]() | 301.6 KB | Display | |
Data in CIF | ![]() | 396 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ir5C ![]() 8ir7C ![]() 8ir8C ![]() 8ir9C ![]() 8iraC ![]() 8irbC ![]() 8ircC ![]() 8irdC ![]() 8ireC ![]() 8irfC ![]() 8irgC ![]() 8irhC ![]() 8iriC 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 AaBbCcDdHhIiJjKkLlMmOoTtUuXxYy...
#1: Protein | Mass: 38235.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 56068.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | Mass: 7227.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Protein/peptide | Mass: 3974.712 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #12: Protein/peptide | Mass: 4009.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #14: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #17: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #18: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #20: Protein/peptide | | Mass: 3859.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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 genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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 genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 33 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)
#31: Sugar | ChemComp-LMT / #34: Sugar | ChemComp-HTG / #35: Sugar | ChemComp-DGD / |
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-Non-polymers , 18 types, 2017 molecules ![](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/GOL.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.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/GOL.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#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-GOL / #28: Chemical | #29: Chemical | ChemComp-PL9 / #30: Chemical | ChemComp-UNL / Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source #32: Chemical | ChemComp-LHG / #33: Chemical | ChemComp-LMG / #36: Chemical | ChemComp-CA / #37: Chemical | #38: Chemical | #39: Chemical | #40: Chemical | #41: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.49 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 5.5% PEG1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.45 Å / Num. obs: 422475 / % possible obs: 100 % / Redundancy: 404.4 % / CC1/2: 0.995 / R split: 0.064 / Net I/σ(I): 56 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 21214 / CC1/2: 0.479 / R split: 0.7589 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.2→19.98 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: 13.9802 Å / Origin y: -14.846 Å / Origin z: -24.5529 Å
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Refinement TLS group | Selection details: all |