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- PDB-5b5n: Crystal structure of the Ba-substituted LH1-RC complex from Tch. ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b5n | ||||||
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Title | Crystal structure of the Ba-substituted LH1-RC complex from Tch. tepidum | ||||||
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![]() | PHOTOSYNTHESIS / Bacterial photosynthesis / Light-harvesting complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang-Otomo, Z.-Y. / Yu, L.-J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 23.5 MB | Display | ![]() |
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Full document | ![]() | 24.1 MB | Display | |
Data in XML | ![]() | 291.4 KB | Display | |
Data in CIF | ![]() | 333.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b5mC ![]() 3wmmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() #2: Protein | Mass: 31520.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 35975.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-319 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 28213.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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) ![]() #6: Protein/peptide | Mass: 5534.452 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 12 types, 190 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/BA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/PEF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MQ8.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BA.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/PEF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MQ8.gif)
![](data/chem/img/CRT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PGW.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |