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Yorodumi- PDB-5b5n: Crystal structure of the Ba-substituted LH1-RC complex from Tch. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b5n | ||||||
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Title | Crystal structure of the Ba-substituted LH1-RC complex from Tch. tepidum | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Bacterial photosynthesis / Light-harvesting complex | ||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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 / Resolution: 3.3 Å | ||||||
Authors | Wang-Otomo, Z.-Y. / Yu, L.-J. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Basis for the Unusual Qy Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum. Authors: Yu, L.J. / Kawakami, T. / Kimura, Y. / Wang-Otomo, Z.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5n.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5b5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5n ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5n | HTTPS FTP |
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-Related structure data
Related structure data | 5b5mC 3wmmS C: citing same article (ref.) 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
-Photosynthetic reaction center ... , 4 types, 8 molecules CoLxMyHt
#1: Protein | Mass: 36630.484 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-333 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P5 #2: Protein | Mass: 31520.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P3 #3: Protein | Mass: 35975.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-319 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A8ASG6 #4: Protein | Mass: 28213.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P9 |
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-Protein / Protein/peptide , 2 types, 64 molecules ADFIKOQSUWY13579mpruwAAACAEAGAIAKdfh...
#5: Protein | Mass: 7034.442 Da / Num. of mol.: 32 / 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.: 32 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1 |
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-Non-polymers , 12 types, 190 molecules
#7: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-BA / #9: Chemical | ChemComp-BCL / #10: Chemical | ChemComp-BPH / #11: Chemical | #12: Chemical | ChemComp-PEF / #13: Chemical | #14: Chemical | #15: Chemical | ChemComp-CRT / #16: Chemical | ChemComp-PO4 / #17: Chemical | #18: 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: 3.14 Å3/Da / Density % sol: 60.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, barium chloride, decylphosphocholine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→49.9 Å / Num. obs: 133051 / % possible obs: 93 % / Redundancy: 22.8 % / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.3→3.36 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMM Resolution: 3.3→49.9 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→49.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.59 Å / Origin y: -15.8433 Å / Origin z: 49.1244 Å
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Refinement TLS group | Selection details: all |