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Yorodumi- PDB-5nj4: From macrocrystals to microcrystals: a strategy for membrane prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nj4 | ||||||
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Title | From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / membrane photosynthetic wild-type XFEL | ||||||
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 | Dods, R. / Baath, P. / Branden, G. / Neutze, R. | ||||||
Citation | Journal: Structure / Year: 2017 Title: From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography. Authors: Dods, R. / Bath, P. / Arnlund, D. / Beyerlein, K.R. / Nelson, G. / Liang, M. / Harimoorthy, R. / Berntsen, P. / Malmerberg, E. / Johansson, L. / Andersson, R. / Bosman, R. / Carbajo, S. / ...Authors: Dods, R. / Bath, P. / Arnlund, D. / Beyerlein, K.R. / Nelson, G. / Liang, M. / Harimoorthy, R. / Berntsen, P. / Malmerberg, E. / Johansson, L. / Andersson, R. / Bosman, R. / Carbajo, S. / Claesson, E. / Conrad, C.E. / Dahl, P. / Hammarin, G. / Hunter, M.S. / Li, C. / Lisova, S. / Milathianaki, D. / Robinson, J. / Safari, C. / Sharma, A. / Williams, G. / Wickstrand, C. / Yefanov, O. / Davidsson, J. / DePonte, D.P. / Barty, A. / 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 | 5nj4.cif.gz | 283.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nj4.ent.gz | 222.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nj4_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 5nj4_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5nj4_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 5nj4_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/5nj4 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/5nj4 | HTTPS FTP |
-Related structure data
Related structure data | 5o4cC 5o64C 2i5nS 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 on special symmetry positions |
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-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 |
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-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 |
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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 , 11 types, 185 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-FE2 / | #13: Chemical | ChemComp-MQ7 / | #14: Chemical | ChemComp-NS5 / | #15: 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 grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 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 ...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 |
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-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.307 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.307 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35.7 Å / Num. obs: 118454 / % possible obs: 100 % / Redundancy: 1529 % / CC1/2: 0.997 / R split: 0.0486 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 106 % / CC1/2: 0.438 / R split: 1.06 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I5N Resolution: 2.4→35.7 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.79 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.496 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→35.7 Å
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