+Open data
-Basic information
Entry | Database: PDB / ID: 4il6 | |||||||||
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Title | Structure of Sr-substituted photosystem II | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Photosystem II / Electron transfer / Light-Driven Water Oxidation / Membrane-Protein Complex / Oxygen Evolution / Oxygen-Evolving Complex / Proton-Coupled Electron Transfer / Photosynthesis / Reaction Centre / Sr-Substituted Photosystem II / Substrate Water molecule / Trans-Membrane Alpha Helix | |||||||||
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 vulcanus (bacteria) Thermosynechococcus elongatus BP-1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Koua, F.H.M. / Umena, Y. / Kawakami, K. / Kamiya, N. / Shen, J.R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation Authors: Koua, F.H. / Umena, Y. / Kawakami, K. / Shen, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4il6.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4il6.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 4il6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4il6_validation.pdf.gz | 32.5 MB | Display | wwPDB validaton report |
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Full document | 4il6_full_validation.pdf.gz | 33.1 MB | Display | |
Data in XML | 4il6_validation.xml.gz | 302.2 KB | Display | |
Data in CIF | 4il6_validation.cif.gz | 376.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/4il6 ftp://data.pdbj.org/pub/pdb/validation_reports/il/4il6 | HTTPS FTP |
-Related structure data
Related structure data | 3arc 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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Unit cell |
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Details | biological unit is the same as asym. |
-Components
-Protein , 2 types, 4 molecules AaVv
#1: Protein | Mass: 37029.234 Da / Num. of mol.: 2 / Fragment: UNP residues 11-344 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II #16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Fragment: UNP residues 27-163 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387 |
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-Photosystem II ... , 16 types, 31 molecules BbCcDdHhIiJjKkLlMmOoTtUuYyXxZzR
#2: Protein | Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1*PLUS #3: Protein | Mass: 49207.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7*PLUS #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8*PLUS, photosystem II #7: Protein | Mass: 7057.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19052*PLUS #8: Protein/peptide | Mass: 4195.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240*PLUS #9: Protein/peptide | Mass: 3756.439 Da / Num. of mol.: 2 / Fragment: UNP residues 4-40 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q7DGD4 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19054*PLUS #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241 #12: Protein/peptide | Mass: 3835.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312*PLUS #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR2*PLUS #14: Protein/peptide | Mass: 3777.559 Da / Num. of mol.: 2 / Fragment: UNP residues 2-31 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313 #15: Protein | Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152*PLUS #17: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3*PLUS #18: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4*PLUS #19: Protein | Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5*PLUS #20: Protein/peptide | | Mass: 3859.732 Da / Num. of mol.: 1 / Fragment: UNP residues 2-35 / Source method: isolated from a natural source / Details: Cell Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / References: UniProt: Q8DKM3 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9192.334 Da / Num. of mol.: 2 / Fragment: UNP residues 4-83 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238 #6: Protein/peptide | Mass: 3868.611 Da / Num. of mol.: 2 / Fragment: UNP residues 12-45 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239 |
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-Sugars , 3 types, 40 molecules
#32: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-HTG / #36: Sugar | ChemComp-DGD / |
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-Non-polymers , 17 types, 2256 molecules
#21: Chemical | #22: Chemical | #23: Chemical | ChemComp-CL / #24: Chemical | ChemComp-CLA / #25: Chemical | ChemComp-PHO / #26: Chemical | ChemComp-BCR / #27: Chemical | ChemComp-PL9 / #28: Chemical | ChemComp-SQD / #29: Chemical | ChemComp-LMG / #30: Chemical | ChemComp-DMS / #31: Chemical | ChemComp-UNL / Num. of mol.: 24 / Source method: obtained synthetically #33: Chemical | ChemComp-GOL / #34: Chemical | ChemComp-LHG / #37: Chemical | #38: Chemical | ChemComp-HEM / #39: Chemical | ChemComp-MG / #40: Water | ChemComp-HOH / | |
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-Details
Sequence details | PRO279/CHAIN A(a) and LEU8/CHAIN M(m) HAVE BEEN CONFIRMED FROM THE ELECTRON DENSITY MAP. SEQUENCES ...PRO279/CHAIN A(a) and LEU8/CHAIN M(m) HAVE BEEN CONFIRMED FROM THE ELECTRON DENSITY MAP. SEQUENCES FOR THE CHAINS B(b), C(c), D(d), REMARK 999 H(h), I(i), K(k), M(m), O(o), U(u), Y(y), X(x), Z(z) ARE BASED ON BOTH ELECTRON DENSITY MAP AND THE SEQUENCES FROM THE CLOSELY RELATED SOURCE THERMOSYNE |
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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: 3.39 Å3/Da / Density % sol: 63.72 % |
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Crystal grow | Temperature: 285 K / Method: oil-microbatch method / pH: 6.1 Details: Sr-PSII protein was crystallised in 4.5-5.5%PEG1450, 20mM Mes-NaOH, pH 6.1, 20mM NaCl, 3-4mM SrCl2, Oil-Microbatch Method, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.76 Å |
Detector | Type: MAR225HE / Detector: CCD / Date: Jun 17, 2011 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.76 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 460677 / Num. obs: 437644 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / Num. unique all: 460678 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ARC 3arc Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.367 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.184 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.41 Å2 / Biso mean: 37.6797 Å2 / Biso min: 16.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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