+Open data
-Basic information
Entry | Database: PDB / ID: 7cji | |||||||||
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Title | Photosystem II structure in the S1 state | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem II | |||||||||
Function / homology | Function and homology information 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 / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Li, H. / Shen, J.-R. / Suga, M. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Iucrj / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cji.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7cji.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 7cji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cji_validation.pdf.gz | 32 MB | Display | wwPDB validaton report |
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Full document | 7cji_full_validation.pdf.gz | 32.8 MB | Display | |
Data in XML | 7cji_validation.xml.gz | 282.8 KB | Display | |
Data in CIF | 7cji_validation.cif.gz | 358.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/7cji ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cji | HTTPS FTP |
-Related structure data
Related structure data | 7cjjC 7couC 5ws5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) Thermosynechococcus 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) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1 #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7 #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II #7: Protein | Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus 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) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240 #9: Protein/peptide | Mass: 3974.712 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus 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) Thermosynechococcus 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) Thermosynechococcus 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) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312 #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus 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) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313 #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152 #17: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4 #18: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3 #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5 #20: Protein/peptide | | Mass: 3859.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0DM37 |
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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) Thermosynechococcus 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) Thermosynechococcus 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) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387 |
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-Sugars , 3 types, 33 molecules
#33: Sugar | ChemComp-HTG / #34: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-DGD / |
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-Non-polymers , 18 types, 2234 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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