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Yorodumi- PDB-5m7l: Blastochloris viridis photosynthetic reaction center synchrotron ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m7l | ||||||
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Title | Blastochloris viridis photosynthetic reaction center synchrotron structure | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosynthetic / Reaction Center | ||||||
Function / homology | Function and homology information 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Blastochloris viridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Sharma, A.S. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G. | ||||||
Citation | Journal: Acta Crystallogr A Found Adv / Year: 2017 Title: Asymmetry in serial femtosecond crystallography data. Authors: Sharma, A. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m7l.cif.gz | 518.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m7l.ent.gz | 419.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/5m7l ftp://data.pdbj.org/pub/pdb/validation_reports/m7/5m7l | HTTPS FTP |
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-Related structure data
Related structure data | 5m7jC 5m7kC 4casS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173 |
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-Reaction center protein ... , 3 types, 3 molecules BCD
#2: Protein | Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009 |
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#3: Protein | Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010 |
#4: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008 |
-Non-polymers , 10 types, 20 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-BCL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-MQ7 / | #12: Chemical | ChemComp-NS5 / | #13: Chemical | ChemComp-OTP / ( | #14: Chemical | |
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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: 63.69 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a ...Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a glass vial and sponge-phase-inducing solution (1:4 ratio) was added containing 16% Jeffamine M-600, 1M HEPES pH 7.9, 0.7 M Ammonium sulphate, 2.5% 1,2,3-Heptanetriol, which swell the cubic phase to sponge phase. After phase separation overnight, the upper phase (sponge phase) was harvested. Crystals were grown using batch crystallization in the lipidic-sponge phase. Equal amount of sponge phase and protein were mixed with 2/5 (v/v) of 1.2 M Tris-sodium citrate and allowed to incubate for several weeks. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.58→50.502 Å / Num. obs: 22398 / % possible obs: 98.9 % / Redundancy: 7 % / Net I/σ(I): 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CAS Resolution: 3.6→50.502 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→50.502 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: 1.6799 Å / Origin y: -19.6761 Å / Origin z: -53.1456 Å
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Refinement TLS group | Selection details: all |