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Yorodumi- PDB-7q7p: LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q7p | |||||||||
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Title | LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / CRYSTALLOGRAPHY STRUCTURE PHOTHOSYNTHETIC REACTION CENTRE | |||||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Baath, P. / Banacore, A. / Neutze, R. | |||||||||
Funding support | European Union, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre. Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M. ...Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M.J. / Vallejos, A. / Ostojic, L. / Edlund, P. / Linse, J.B. / Andersson, R. / Nango, E. / Owada, S. / Tanaka, R. / Tono, K. / Joti, Y. / Nureki, O. / Luo, F. / James, D. / Nass, K. / Johnson, P.J.M. / Knopp, G. / Ozerov, D. / Cirelli, C. / Milne, C. / Iwata, S. / Branden, G. / Neutze, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q7p.cif.gz | 292.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q7p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q7p_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7q7p_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7q7p_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 7q7p_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/7q7p ftp://data.pdbj.org/pub/pdb/validation_reports/q7/7q7p | HTTPS FTP |
-Related structure data
Related structure data | 7q7qC 2i5nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 CCC
#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 HHHLLLMMM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008 |
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#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009 |
#4: Protein | Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010 |
-Non-polymers , 13 types, 278 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-HTO / #8: Chemical | ChemComp-OLC / ( | #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-BCB / #11: Chemical | #12: Chemical | #13: Chemical | #14: Chemical | ChemComp-FE2 / | #15: Chemical | ChemComp-MQ7 / | #16: Chemical | ChemComp-NS5 / | #17: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.62 Å3/Da / Density % sol: 65.98 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 60:40 monoolein with UQ2, protein 40 mg/mL concentration. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.4 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→73.92 Å / Num. obs: 76977 / % possible obs: 100 % / Redundancy: 7.05 % / CC1/2: 0.994 / R split: 0.1057 / Net I/σ(I): 7.87 |
Reflection shell | Resolution: 2.4→2.42 Å / Num. unique obs: 76977 / CC1/2: 0.42 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I5N Resolution: 2.4→73.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.447 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.188 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→73.92 Å
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Refine LS restraints |
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LS refinement shell |
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