[English] 日本語
Yorodumi- PDB-6zi5: Ultrafast Structural Response to Charge Redistribution Within a P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zi5 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Ultrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 300 ps (a) structure | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | ELECTRON TRANSPORT / ELECTRON TRANSPORT Photosynthesis Membrane Protein | ||||||||||||||||||
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: 2.8 Å | ||||||||||||||||||
Authors | Baath, P. / Dods, R. / Braenden, G. / Neutze, R. | ||||||||||||||||||
Funding support | United States, Sweden, Finland, 5items
| ||||||||||||||||||
Citation | Journal: Nature / Year: 2021 Title: Ultrafast structural changes within a photosynthetic reaction centre. Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / ...Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / Milathianaki, D. / Robinson, J. / Harimoorthy, R. / Berntsen, P. / Malmerberg, E. / Johansson, L. / Andersson, R. / Carbajo, S. / Claesson, E. / Conrad, C.E. / Dahl, P. / Hammarin, G. / Hunter, M.S. / Li, C. / Lisova, S. / Royant, A. / Safari, C. / Sharma, A. / Williams, G.J. / Yefanov, O. / Westenhoff, S. / Davidsson, J. / DePonte, D.P. / Boutet, S. / Barty, A. / Katona, G. / Groenhof, G. / Branden, G. / Neutze, R. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zi5.cif.gz | 342.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zi5.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 6zi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zi5_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6zi5_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 6zi5_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 6zi5_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/6zi5 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zi5 | HTTPS FTP |
-Related structure data
Related structure data | 6zhwC 6zi4C 6zi6C 6zi9C 6ziaC 6zidC 2i5nS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1726093 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173 |
---|
-Reaction center protein ... , 3 types, 3 molecules HLM
#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 |
---|---|
#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 , 11 types, 45 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-DGA / | #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-LDA / #9: Chemical | #10: Chemical | ChemComp-BCB / #11: Chemical | #12: Chemical | ChemComp-FE / | #13: Chemical | ChemComp-MQ7 / | #14: Chemical | ChemComp-NS5 / | #15: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant ...Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant Microcrystals: 8.5 mg/ml protein 18.5 ul sitting drop, 10 protein : 7.5 precipitant : 1 seed stock |
---|
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.89 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.8 Å / Num. obs: 73191 / % possible obs: 100 % / Redundancy: 1133 % / Biso Wilson estimate: 103.26 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 2.8→2.86 Å / Mean I/σ(I) obs: 0.88 / Num. unique obs: 4824 / CC1/2: 0.345 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I5N Resolution: 2.8→37.75 Å / SU ML: 0.3468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.168 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|