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Yorodumi- PDB-5y5s: Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y5s | |||||||||
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Title | Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LH1-RC / purple bacteria | |||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Thermochromatium tepidum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | |||||||||
Authors | Yu, L.-J. / Suga, M. / Wang-Otomo, Z.-Y. / Shen, J.-R. | |||||||||
Citation | Journal: Nature / Year: 2018 Title: Structure of photosynthetic LH1-RC supercomplex at 1.9 angstrom resolution. Authors: Yu, L.-J. / Suga, M. / Wang-Otomo, Z.-Y. / 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 | 5y5s.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5y5s.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 5y5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y5s_validation.pdf.gz | 23.4 MB | Display | wwPDB validaton report |
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Full document | 5y5s_full_validation.pdf.gz | 23.7 MB | Display | |
Data in XML | 5y5s_validation.xml.gz | 169.6 KB | Display | |
Data in CIF | 5y5s_validation.cif.gz | 195.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/5y5s ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y5s | HTTPS FTP |
-Related structure data
Related structure data | 3wmmS 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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Components on special symmetry positions |
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-Components
-Photosynthetic reaction center ... , 4 types, 4 molecules CLMH
#1: Protein | Mass: 43177.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P5 |
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#2: Protein | Mass: 31520.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P3 |
#3: Protein | Mass: 36605.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A8ASG6 |
#4: Protein | Mass: 28213.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P9 |
-Protein / Protein/peptide / Sugars , 3 types, 34 molecules ADFIKOQSUWY13579BEGJNPRTVXZ246...
#23: Sugar | #5: Protein | Mass: 7034.442 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P2 #6: Protein/peptide | Mass: 5534.452 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1 |
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-Non-polymers , 18 types, 1096 molecules
#7: Chemical | ChemComp-HEC / #8: Chemical | ChemComp-MG / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-LHG / | #12: Chemical | ChemComp-PGV / ( #13: Chemical | ChemComp-BCL / #14: Chemical | #15: Chemical | ChemComp-UQ8 / #16: Chemical | ChemComp-UNL / Num. of mol.: 16 / Source method: obtained synthetically #17: Chemical | ChemComp-FE / | #18: Chemical | ChemComp-MQ8 / | #19: Chemical | ChemComp-CRT / #20: Chemical | ChemComp-PEF / #21: Chemical | ChemComp-LDA / #22: Chemical | ChemComp-CDL / #24: Chemical | ChemComp-CA / #25: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | UNL IN THIS STRUCTURE WAS TUBE-LIKE ELECTRON DENSITY, MIGHT BE A TAIL OF LIPID OR DETERGENT, WHICH ...UNL IN THIS STRUCTURE WAS TUBE-LIKE ELECTRON DENSITY, MIGHT BE A TAIL OF LIPID OR DETERGENT, WHICH COULD NOT BE ASSIGNED UNAMBIGUOU |
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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: 3.22 Å3/Da / Density % sol: 61.85 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: PEG 1450, calcium chloride, octyl-phosphocholine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.919 Å / Num. obs: 338604 / % possible obs: 99.95 % / Redundancy: 9.2 % / Biso Wilson estimate: 39.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1035 / Rpim(I) all: 0.035 / Net I/σ(I): 9.47 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 33819 / CC1/2: 0.557 / Rpim(I) all: 0.6936 / % possible all: 99.98 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMM Resolution: 1.9→46.919 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.55 / Stereochemistry target values: ML
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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 max: 165.53 Å2 / Biso mean: 65.4864 Å2 / Biso min: 26.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→46.919 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -40.6459 Å / Origin y: 30.5496 Å / Origin z: 52.8476 Å
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Refinement TLS group |
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