[English] 日本語
Yorodumi- PDB-6dhf: RT XFEL structure of the one-flash state of Photosystem II (1F, S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dhf | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RT XFEL structure of the one-flash state of Photosystem II (1F, S2-rich) at 2.08 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Keywords | PHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 elongatus (bacteria) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. ...Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seufert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | United States, Germany, Sweden, United Kingdom, 21items
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Citation | Journal: Nature / Year: 2018 Title: Structures of the intermediates of Kok's photosynthetic water oxidation clock. Authors: Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de ...Authors: Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seuffert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dhf.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dhf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6dhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dhf_validation.pdf.gz | 31.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dhf_full_validation.pdf.gz | 31.8 MB | Display | |
Data in XML | 6dhf_validation.xml.gz | 271.5 KB | Display | |
Data in CIF | 6dhf_validation.cif.gz | 347.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/6dhf ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dhf | HTTPS FTP |
-Related structure data
Related structure data | 6dheC 6dhgC 6dhhC 6dhoC 6dhpC 5kafS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...
#1: Protein | Mass: 37059.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A444, photosystem II #2: Protein | Mass: 56096.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIQ1 #3: Protein | Mass: 49207.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIF8 #4: Protein | Mass: 38275.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8CM25, photosystem II #7: Protein | Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4195.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6 #9: Protein/peptide | Mass: 3627.325 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P59087 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 3706.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7 #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A431 #14: Protein/peptide | Mass: 3648.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0 #15: Protein | Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1L5 #17: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DJI1 #18: Protein/peptide | Mass: 3990.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q9F1R6 #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DHJ2 #20: Protein/peptide | Mass: 3859.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DKM3 |
---|
-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9378.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 3868.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: Q8DIN9 |
---|
-Protein / Sugars , 2 types, 12 molecules Vv
#16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / References: UniProt: P0A386 #29: Sugar | ChemComp-DGD / |
---|
-Non-polymers , 15 types, 2193 molecules
#21: Chemical | #22: Chemical | ChemComp-CL / #23: Chemical | #24: Chemical | ChemComp-CLA / #25: Chemical | ChemComp-PHO / #26: Chemical | ChemComp-BCR / #27: Chemical | ChemComp-PL9 / #28: Chemical | ChemComp-SQD / #30: Chemical | #31: Chemical | ChemComp-UNL / Mass: 787.158 Da / Num. of mol.: 31 / Source method: obtained synthetically #32: Chemical | ChemComp-LMG / #33: Chemical | ChemComp-LHG / #34: Chemical | #35: Chemical | #36: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.48 % / Description: Cube-like crystals |
---|---|
Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000 |
-Data collection
Diffraction |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→30.43 Å / Num. obs: 472399 / % possible obs: 99.96 % / Redundancy: 211.04 % / CC1/2: 0.975 / Net I/σ(I): 14.999 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Serial crystallography measurement | Focal spot size: 3 µm2 / Pulse duration: 40 fsec. / Pulse energy: 3.55 µJ / Pulse photon energy: 9.515 keV / XFEL pulse repetition rate: 10 Hz | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Serial crystallography sample delivery | Method: fixed target | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Serial crystallography data reduction | Frames total: 114690 / Lattices indexed: 10568 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KAF Resolution: 2.08→30.427 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.65
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.34 Å2 / Biso mean: 46.9236 Å2 / Biso min: 12.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→30.427 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
|