[English] 日本語
![](img/lk-miru.gif)
- PDB-7rf5: RT XFEL structure of Photosystem II 150 microseconds after the se... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7rf5 | |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution | |||||||||||||||||||||||||||||||||||||||
![]() |
| |||||||||||||||||||||||||||||||||||||||
![]() | PHOTOSYNTHESIS / Membrane protein | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() 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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
![]() | Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M.D. / Bogacz, I. / Kim, I.-S. / Cheah, M.H. ...Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M.D. / Bogacz, I. / Kim, I.-S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, C.C. / Young, I.D. / Carbajo, S. / Fuller, F.D. / Alonso-Mori, R. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bolotovski, R. / Mendez, D. / Holton, J.M. / Moriarty, N.W. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Dobbek, H. / Messinger, J. / Zouni, A. / Kern, J. / Yachandra, V.K. / Yano, J. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
| |||||||||||||||||||||||||||||||||||||||
![]() | ![]() Title: Structural dynamics in the water and proton channels of photosystem II during the S 2 to S 3 transition. Authors: Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M. / Bogacz, I. / Kim, I.S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, ...Authors: Hussein, R. / Ibrahim, M. / Bhowmick, A. / Simon, P.S. / Chatterjee, R. / Lassalle, L. / Doyle, M. / Bogacz, I. / Kim, I.S. / Cheah, M.H. / Gul, S. / de Lichtenberg, C. / Chernev, P. / Pham, C.C. / Young, I.D. / Carbajo, S. / Fuller, F.D. / Alonso-Mori, R. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bolotovsky, R. / Mendez, D. / Holton, J.M. / Moriarty, N.W. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Dobbek, H. / Messinger, J. / Zouni, A. / Kern, J. / Yachandra, V.K. / Yano, J. | |||||||||||||||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7rf1C ![]() 7rf2C ![]() 7rf3C ![]() 7rf4C ![]() 7rf6C ![]() 7rf7C ![]() 7rf8C ![]() 6dheS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A444, photosystem II #2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIQ1 #3: Protein | Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIF8 #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8CM25, photosystem II #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJZ6 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P59087 #10: Protein/peptide | Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DHA7 #13: Protein | Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A431 #14: Protein/peptide | Mass: 4590.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DKM3 #15: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIQ0 #16: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1L5 #18: Protein/peptide | Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1R6 #19: Protein/peptide | Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJI1 #20: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DHJ2 |
---|
-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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN9 |
---|
-Protein / Sugars , 2 types, 11 molecules Vv![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#17: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A386 #31: Sugar | ChemComp-DGD / |
---|
-Non-polymers , 16 types, 1607 molecules ![](data/chem/img/OEY.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/STE.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/STE.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#21: Chemical | #22: Chemical | #23: Chemical | #24: Chemical | ChemComp-CLA / #25: Chemical | ChemComp-PHO / #26: Chemical | ChemComp-BCR / #27: Chemical | ChemComp-CL / #28: Chemical | ChemComp-PL9 / #29: Chemical | ChemComp-SQD / #30: Chemical | ChemComp-LHG / #32: Chemical | ChemComp-STE / #33: Chemical | ChemComp-LMG / #34: Chemical | #35: Chemical | #36: Chemical | #37: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.19 % |
---|---|
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 | Mean temperature: 298 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Nov 27, 2018 / Frequency: 20 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.30219 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→33.7 Å / Num. obs: 386505 / % possible obs: 99.6 % / Redundancy: 48.1 % / Biso Wilson estimate: 39.13 Å2 / CC1/2: 0.965 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.23→2.27 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 18749 / CC1/2: 0.056 / % possible all: 97.52 |
Serial crystallography measurement | Collimation: Compound Refractive Lenses / Focal spot size: 3 µm2 / Pulse duration: 40 fsec. / Pulse energy: 3 µJ / Pulse photon energy: 9520 keV / XFEL pulse repetition rate: 20 Hz |
Serial crystallography sample delivery | Description: Drop-on-Tape / Method: injection |
Serial crystallography sample delivery injection | Description: Acoustic Droplet Ejection / Flow rate: 4 µL/min / Power by: Acoustic Wave |
Serial crystallography data reduction | Lattices indexed: 6195 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6DHE Resolution: 2.23→33.7 Å / SU ML: 0.3445 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7858 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→33.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|