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- PDB-6dhg: RT XFEL structure of Photosystem II 150 microseconds after the se... -
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Basic information
Entry | Database: PDB / ID: 6dhg | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Title | RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.5 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | PHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
![]() | 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 | ![]() ![]() ![]() ![]()
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![]() | ![]() 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. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. #3: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: DIALS: implementation and evaluation of a new integration package. Authors: Winter, G. / Waterman, D.G. / Parkhurst, J.M. / Brewster, A.S. / Gildea, R.J. / Gerstel, M. / Fuentes-Montero, L. / Vollmar, M. / Michels-Clark, T. / Young, I.D. / Sauter, N.K. / Evans, G. #4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Features and development of Coot. Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan / ![]() Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. #5: ![]() Title: Protein structural ensembles are revealed by redefining X-ray electron density noise. Authors: Lang, P.T. / Holton, J.M. / Fraser, J.S. / Alber, T. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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, 34 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...
#1: Protein | Mass: 37059.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() #9: Protein/peptide | Mass: 3627.325 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() 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) ![]() ![]() #15: Protein | Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DKM3 |
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-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) ![]() ![]() 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Protein / Sugars , 2 types, 12 molecules Vv![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A386 #28: Sugar | ChemComp-DGD / |
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-Non-polymers , 15 types, 2188 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/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HEM.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/PL9.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/OEX.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HEM.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-PL9 / #27: Chemical | ChemComp-SQD / #29: Chemical | ChemComp-LHG / #30: Chemical | #31: Chemical | #32: Chemical | ChemComp-UNL / Mass: 787.158 Da / Num. of mol.: 31 / Source method: obtained synthetically #33: Chemical | ChemComp-LMG / #34: Chemical | #35: Chemical | #36: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.24 % / Description: Cube-like crystals |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX170-HS / Detector: CCD / Date: Jul 13, 2017 / Details: Compound refractive lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.305 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30.78 Å / Num. obs: 279073 / % possible obs: 99.93 % / Redundancy: 61.41 % / CC1/2: 0.938 / Net I/σ(I): 11.143 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Serial crystallography measurement | Focal spot size: 3 µm2 / Pulse duration: 40 fsec. / Pulse energy: 4.51 µJ / Pulse photon energy: 9.53 keV / XFEL pulse repetition rate: 10 Hz | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Serial crystallography sample delivery | Method: fixed target | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Serial crystallography data reduction | Lattices indexed: 4231 |
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Processing
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Refinement | Resolution: 2.5→30.783 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.19 / 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: 193.13 Å2 / Biso mean: 53.8673 Å2 / Biso min: 17.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→30.783 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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