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- PDB-4ixr: RT fs X-ray diffraction of Photosystem II, first illuminated state -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ixr | |||||||||
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Title | RT fs X-ray diffraction of Photosystem II, first illuminated state | |||||||||
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![]() | PHOTOSYNTHESIS / iron / manganese / PS II / PS2 / transmembrane alpha-helix / electron transport / reaction center / water oxidation / membrane complex / thylakoid membrane | |||||||||
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 / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Gloeckner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. ...Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Gloeckner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / Han, G. / Gul, S. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / Schafer, D.W. / Messerschmidt, M. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.-C. / Sellberg, J. / Latimer, M.J. / Grosse-Kunstleve, R.W. / Zwart, P.H. / White, W.E. / Glatzel, P. / Adams, P.D. / Bogan, M.J. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Sauter, N.K. / Yachandra, V.K. / Bergmann, U. / Yano, J. | |||||||||
![]() | ![]() Title: Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Authors: Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / ...Authors: Kern, J. / Alonso-Mori, R. / Tran, R. / Hattne, J. / Gildea, R.J. / Echols, N. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Koroidov, S. / Lampe, A. / Han, G. / Gul, S. / Difiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / Schafer, D.W. / Messerschmidt, M. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.C. / Sellberg, J. / Latimer, M.J. / Grosse-Kunstleve, R.W. / Zwart, P.H. / White, W.E. / Glatzel, P. / Adams, P.D. / Bogan, M.J. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Sauter, N.K. / Yachandra, V.K. / Bergmann, U. / Yano, J. | |||||||||
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 | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 20.1 MB | Display | ![]() |
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Full document | ![]() | 20.5 MB | Display | |
Data in XML | ![]() | 254.2 KB | Display | |
Data in CIF | ![]() | 306.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ixqC ![]() 3bz1 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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1 |
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Unit cell |
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Components
-Protein , 2 types, 4 molecules AaVv
#1: Protein | Mass: 39762.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Photosystem II ... , 16 types, 32 molecules BbCcDdHhIiJjKkLlMmOoTtUuygXxZzGY
#2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein/peptide | Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein/peptide | Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein/peptide | Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 28 molecules ![](data/chem/img/DGD.gif)
![](data/chem/img/LMT.gif)
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#28: Sugar | ChemComp-DGD / #33: Sugar | ChemComp-LMT / |
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-Non-polymers , 13 types, 156 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
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![](data/chem/img/OEC.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/OEC.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
#21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CLA / #24: Chemical | ChemComp-PHO / #25: Chemical | ChemComp-PL9 / #26: Chemical | #27: Chemical | ChemComp-BCR / #29: Chemical | ChemComp-LHG / #30: Chemical | ChemComp-SQD / #31: Chemical | ChemComp-LMG / #32: Chemical | #34: Chemical | ChemComp-HEM / #35: Chemical | ChemComp-CA / |
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-Details
Sequence details | THE SEQUENCE OF CHAINS Y AND G IS KNOWN BUT WAS MODELED AS POLYALANINE DUE TO POOR DENSITY. THE ...THE SEQUENCE OF CHAINS Y AND G IS KNOWN BUT WAS MODELED AS POLYALANIN |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: 4% PEG2000, 5 mM calcium chloride, 100 mM PIPES, pH 7.0, BATCH, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Dec 6, 2011 / Details: KB mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: No monochromator, FEL beam with 20-30 eV bandwidth Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 5.9→83 Å / Num. all: 25059 / Num. obs: 24671 / % possible obs: 98.5 % / Observed criterion σ(I): 4.2 / Redundancy: 22.9 % / Net I/σ(I): 22.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BZ1 ![]() 3bz1 Resolution: 5.9→82.97 Å / SU ML: 0.92 / σ(F): 1.4 / σ(I): 4.2 / Phase error: 30.52 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.9→82.97 Å
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Refine LS restraints |
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LS refinement shell |
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