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Yorodumi- PDB-5mx2: Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mx2 | ||||||||||||
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Title | Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Photosynthesis / Metal Cluster / EDTA / Hydroxylamine / Thermosynechococcus elongatus | ||||||||||||
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 vestitus BP-1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å | ||||||||||||
Authors | Zhang, M. / Bommer, M. / Chatterjee, R. / Hussain, R. / Kern, J. / Yano, J. / Dau, H. / Dobbek, H. / Zouni, A. | ||||||||||||
Funding support | Germany, 1items
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Citation | Journal: Elife / Year: 2017 Title: Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II. Authors: Zhang, M. / Bommer, M. / Chatterjee, R. / Hussein, R. / Yano, J. / Dau, H. / Kern, J. / Dobbek, H. / Zouni, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mx2.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5mx2.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5mx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mx2_validation.pdf.gz | 38 MB | Display | wwPDB validaton report |
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Full document | 5mx2_full_validation.pdf.gz | 38.2 MB | Display | |
Data in XML | 5mx2_validation.xml.gz | 237.6 KB | Display | |
Data in CIF | 5mx2_validation.cif.gz | 300.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mx2 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mx2 | HTTPS FTP |
-Related structure data
Related structure data | 4pj0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus 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 Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) Strain: BP-1 / References: UniProt: P0A431 #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus 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 Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) 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) Thermosynechococcus vestitus BP-1 (bacteria) Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Protein / Sugars , 2 types, 10 molecules Vv
#16: Protein | Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria) Strain: BP-1 / References: UniProt: P0A386 #30: Sugar | ChemComp-DGD / |
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-Non-polymers , 14 types, 884 molecules
#21: Chemical | ChemComp-CL / #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-PHO / #24: Chemical | ChemComp-BCR / #25: Chemical | ChemComp-PL9 / #26: Chemical | ChemComp-SQD / #27: Chemical | ChemComp-LFA / #28: Chemical | #29: Chemical | ChemComp-LMG / #31: Chemical | #32: Chemical | ChemComp-LHG / #33: Chemical | #34: Chemical | #35: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 7.5 Details: equal volumes of buffer: 0.1 M Tris-HCl pH 7.5, 0.1 M (NH4)2SO4, 14-18 % PEG 5000 MME and protein: 2 mM chlorophyll equivalent of PSII in C12E8 detergent, post crystallisation treatment |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2016 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→49.7 Å / Num. obs: 364603 / % possible obs: 93 % / Redundancy: 11.2 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.25 / Net I/σ(I): 9.34 |
Reflection shell | Resolution: 2.197→2.276 Å / Redundancy: 5.2 % / Rmerge(I) obs: 3.27 / Mean I/σ(I) obs: 0.44 / Num. unique obs: 25404 / CC1/2: 0.132 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PJ0 Resolution: 2.197→49.652 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.197→49.652 Å
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Refine LS restraints |
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LS refinement shell |
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