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- PDB-5kai: NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kai | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Title | NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at 2.8 A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | ELECTRON TRANSPORT / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
![]() | Young, I.D. / Ibrahim, M. / Chatterjee, R. / Gul, S. / Koroidov, S. / Brewster, A.S. / Tran, R. / Alonso-Mori, R. / Fuller, F. / Kroll, T. ...Young, I.D. / Ibrahim, M. / Chatterjee, R. / Gul, S. / Koroidov, S. / Brewster, A.S. / Tran, R. / Alonso-Mori, R. / Fuller, F. / Kroll, T. / Michels-Clark, T. / Laksmono, H. / Sierra, R.G. / Stan, C.A. / Saracini, C. / Bean, M.A. / Seuffert, I. / Sokaras, D. / Weng, T.-C. / Hunter, M.S. / Aquila, A. / Koglin, J.E. / Robinson, J. / Liang, M. / Boutet, S. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Moriarty, N.W. / Liebschner, D. / Afonine, P.V. / Waterman, D.G. / Evans, G. / Dobbek, H. / Weis, W.I. / Brunger, A.T. / Zwart, P.H. / Adams, P.D. / Zouni, A. / Messinger, J. / Bergmann, U. / Sauter, N.K. / Kern, J. / Yachandra, V.K. / Yano, J. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]() ![]() ![]()
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![]() | ![]() Title: Structure of photosystem II and substrate binding at room temperature. Authors: Young, I.D. / Ibrahim, M. / Chatterjee, R. / Gul, S. / Fuller, F.D. / Koroidov, S. / Brewster, A.S. / Tran, R. / Alonso-Mori, R. / Kroll, T. / Michels-Clark, T. / Laksmono, H. / Sierra, R.G. ...Authors: Young, I.D. / Ibrahim, M. / Chatterjee, R. / Gul, S. / Fuller, F.D. / Koroidov, S. / Brewster, A.S. / Tran, R. / Alonso-Mori, R. / Kroll, T. / Michels-Clark, T. / Laksmono, H. / Sierra, R.G. / Stan, C.A. / Hussein, R. / Zhang, M. / Douthit, L. / Kubin, M. / de Lichtenberg, C. / Vo Pham, L. / Nilsson, H. / Cheah, M.H. / Shevela, D. / Saracini, C. / Bean, M.A. / Seuffert, I. / Sokaras, D. / Weng, T.C. / Pastor, E. / Weninger, C. / Fransson, T. / Lassalle, L. / Brauer, P. / Aller, P. / Docker, P.T. / Andi, B. / Orville, A.M. / Glownia, J.M. / Nelson, S. / Sikorski, M. / Zhu, D. / Hunter, M.S. / Lane, T.J. / Aquila, A. / Koglin, J.E. / Robinson, J. / Liang, M. / Boutet, S. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Moriarty, N.W. / Liebschner, D. / Afonine, P.V. / Waterman, D.G. / Evans, G. / Wernet, P. / Dobbek, H. / Weis, W.I. / Brunger, A.T. / Zwart, P.H. / Adams, P.D. / Zouni, A. / Messinger, J. / Bergmann, U. / Sauter, N.K. / Kern, J. / Yachandra, V.K. / Yano, J. #1: Journal: Acta Crystallogr.,Sect.D / 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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 28.3 MB | Display | ![]() |
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Full document | ![]() | 28.6 MB | Display | |
Data in XML | ![]() | 233.5 KB | Display | |
Data in CIF | ![]() | 287.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kafC ![]() 5tisC ![]() 4pj0S ![]() 4ub6S C: citing same article ( S: Starting model for refinement |
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Similar 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: 38265.625 Da / Num. of mol.: 2 / Fragment: UNP residues 1-344 / 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: 7057.349 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: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIQ0 #15: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1L5 #17: 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 #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 | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DHJ2 #20: 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 |
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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) ![]() ![]() 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 |
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-Protein / Sugars , 2 types, 10 molecules Vv![](data/chem/img/DGD.gif)
![](data/chem/img/DGD.gif)
#16: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A386 #33: Sugar | ChemComp-DGD / |
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-Non-polymers , 15 types, 279 molecules ![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/LMG.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/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/LMG.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/BCT.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#21: Chemical | #22: Chemical | #23: Chemical | ChemComp-LMG / #24: Chemical | ChemComp-CL / #25: Chemical | ChemComp-CLA / #26: Chemical | ChemComp-PHO / #27: Chemical | ChemComp-BCR / #28: Chemical | ChemComp-PL9 / #29: Chemical | ChemComp-SQD / #30: Chemical | ChemComp-UNL / Mass: 616.487 Da / Num. of mol.: 23 / Source method: obtained synthetically #31: Chemical | #32: Chemical | ChemComp-LHG / #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: 3.71 Å3/Da / Density % sol: 66.86 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.5 Details: Crystal growth was as described in Kern et al. 2005, Biochim. Biophys. Acta-Bioenergetics and Ibrahim et al. 2015, Struct. Dyn. 2 (4), 041705, substituting C12E8 for beta-DM and Betaine for glycerol |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 28, 2014 / Details: 1 micron KB mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7492 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→43.569812 Å / Num. obs: 213400 / % possible obs: 99 % / Redundancy: 13.7 % / Biso Wilson estimate: 60.4069710515 Å2 / CC1/2: 0.524 / Net I/σ(I): 11.62 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PSII monomer composed of 4UB6 monomer and additional chain from 4PJ0 Resolution: 2.80000914773→43.5698116774 Å / SU ML: 0.504121620111 / Cross valid method: FREE R-VALUE / σ(F): 1.32517238381 / Phase error: 34.5352448831 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 56.5229924032 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.80000914773→43.5698116774 Å
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Refine LS restraints |
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LS refinement shell |
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