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Open data
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Basic information
Entry | Database: PDB / ID: 7cji | |||||||||
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Title | Photosystem II structure in the S1 state | |||||||||
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![]() | PHOTOSYNTHESIS / Photosystem II | |||||||||
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. / Shen, J.-R. / Suga, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Capturing structural changes of the S 1 to S 2 transition of photosystem II using time-resolved serial femtosecond crystallography. Authors: Li, H. / Nakajima, Y. / Nomura, T. / Sugahara, M. / Yonekura, S. / Chan, S.K. / Nakane, T. / Yamane, T. / Umena, Y. / Suzuki, M. / Masuda, T. / Motomura, T. / Naitow, H. / Matsuura, Y. / ...Authors: Li, H. / Nakajima, Y. / Nomura, T. / Sugahara, M. / Yonekura, S. / Chan, S.K. / Nakane, T. / Yamane, T. / Umena, Y. / Suzuki, M. / Masuda, T. / Motomura, T. / Naitow, H. / Matsuura, Y. / Kimura, T. / Tono, K. / Owada, S. / Joti, Y. / Tanaka, R. / Nango, E. / Akita, F. / Kubo, M. / Iwata, S. / Shen, J.R. / Suga, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | 2.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 32 MB | Display | ![]() |
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Full document | ![]() | 32.8 MB | Display | |
Data in XML | ![]() | 282.8 KB | Display | |
Data in CIF | ![]() | 358.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cjjC ![]() 7couC ![]() 5ws5S S: Starting model for refinement C: citing same article ( |
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Similar 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 ... , 17 types, 33 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuXxYy...
#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 / Source: (natural) ![]() #9: Protein/peptide | Mass: 3974.712 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: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein/peptide | Mass: 3228.035 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) ![]() #20: Protein/peptide | | Mass: 3859.732 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: 9580.840 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, 33 molecules ![](data/chem/img/HTG.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
#33: Sugar | ChemComp-HTG / #34: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-DGD / |
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-Non-polymers , 18 types, 2234 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/GOL.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.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/GOL.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.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-GOL / #27: Chemical | ChemComp-SQD / #28: Chemical | #29: Chemical | ChemComp-PL9 / #30: Chemical | ChemComp-UNL / Mass: 618.503 Da / Num. of mol.: 18 / Source method: obtained synthetically #31: Chemical | ChemComp-LMG / #32: Chemical | ChemComp-LHG / #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 | N |
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Nonpolymer details | Ligands assigned with UNL cannot be identified and were built as lipids or detergents. |
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 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.73 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: PEG, magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Apr 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 351162 / % possible obs: 100 % / Redundancy: 494 % / Biso Wilson estimate: 52.01 Å2 / CC1/2: 0.999 / Net I/σ(I): 56.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 339 % / Mean I/σ(I) obs: 2 / Num. unique obs: 34826 / CC1/2: 0.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ws5 Resolution: 2.35→39.932 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.05 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196 Å2 / Biso mean: 67.0154 Å2 / Biso min: 35.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→39.932 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 13.6366 Å / Origin y: -14.3831 Å / Origin z: -25.581 Å
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Refinement TLS group |
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