+Open data
-Basic information
Entry | Database: PDB / ID: 5b5e | |||||||||
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Title | Crystal structure analysis of Photosystem II complex | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / PHOTOSYNTHESIS / psii / photosystem / membrane complex / transmembrane alpha-helix / oxygen evolving / water splitting / iron binding / calcium binding / manganese binding / chloride binding / formylation / hydroxylation / thylakoid membrane | |||||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / 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 / photosynthetic electron transport in photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å | |||||||||
Authors | Tanaka, A. / Fukushima, Y. / Kamiya, N. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II Authors: Tanaka, A. / Fukushima, Y. / Kamiya, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5e.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5e.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5b5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Photosystem II ... , 16 types, 32 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXxZz
#1: Protein | Mass: 38235.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II #2: Protein | Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1 #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7 #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8, photosystem II #7: Protein | Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19052 #8: Protein/peptide | Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FME 1 (Modified residue: N-FORMYLMETHIONINE) / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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 / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19054 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241 #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312 #13: Protein | Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR2 #14: Protein/peptide | Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FME 1 (Modified residue: N-FORMYLMETHIONINE) / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313 #15: Protein | Mass: 11655.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152 #17: Protein/peptide | Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3 #18: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4 #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9449.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238 #6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239 |
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-Protein , 1 types, 2 molecules Vv
#16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387 |
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-Sugars , 3 types, 46 molecules
#30: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-HTG / #36: Sugar | ChemComp-DGD / |
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-Non-polymers , 19 types, 3944 molecules
#20: Chemical | #21: Chemical | #22: Chemical | ChemComp-CL / #23: Chemical | ChemComp-CLA / #24: Chemical | ChemComp-PHO / #25: Chemical | ChemComp-BCR / #26: Chemical | ChemComp-SQD / #27: Chemical | ChemComp-PL9 / #28: Chemical | ChemComp-LHG / #29: Chemical | ChemComp-UNL / Num. of mol.: 53 / Source method: obtained synthetically #31: Chemical | ChemComp-DMS / #32: Chemical | #33: Chemical | ChemComp-CA / #34: Chemical | ChemComp-LMG / #37: Chemical | #38: Chemical | #39: Chemical | #40: Chemical | #41: Water | ChemComp-HOH / | |
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-Details
Sequence details | ABOUT PRO A(a) 279, LEU K(k) 33, TRP K(k) 39 AND LEU M(m) 8, THE AUTHOR CONFIRMED BY ELECTRON ...ABOUT PRO A(a) 279, LEU K(k) 33, TRP K(k) 39 AND LEU M(m) 8, THE AUTHOR CONFIRMED BY ELECTRON DENSITY MAP. SEQUENCE DIFFERENCE |
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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: 3.35 Å3/Da / Density % sol: 63.27 % |
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Crystal grow | Temperature: 285 K / Method: microbatch / pH: 6.1 / Details: Mes,NaCl,CaCl2,MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→49 Å / Num. obs: 649016 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.2 |
-Processing
Software |
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Refinement | Resolution: 1.87→48.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.165 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 33.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→48.98 Å
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