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Yorodumi- PDB-7q38: Crystal structure of the mutant bacteriorhodopsin pressurized wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q38 | ||||||
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Title | Crystal structure of the mutant bacteriorhodopsin pressurized with argon | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / proton pump rhodopsin | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Melnikov, I. / Rulev, M. / Astashkin, R. / Kovalev, K. / Carpentier, P. / Gordeliy, V. / Popov, A. | ||||||
Funding support | 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / ...Authors: Melnikov, I. / Orekhov, P. / Rulev, M. / Kovalev, K. / Astashkin, R. / Bratanov, D. / Ryzhykau, Y. / Balandin, T. / Bukhdruker, S. / Okhrimenko, I. / Borshchevskiy, V. / Bourenkov, G. / Mueller-Dieckmann, C. / van der Linden, P. / Carpentier, P. / Leonard, G. / Gordeliy, V. / Popov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q38.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q38.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 7q38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q38 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q38 | HTTPS FTP |
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-Related structure data
Related structure data | 7q35C 7q36C 7q37C 4xxjS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29045.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halophile) Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: bop, VNG_1467G / Production host: Escherichia coli (E. coli) / References: UniProt: P02945 |
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-Non-polymers , 8 types, 187 molecules
#2: Chemical | ChemComp-RET / | ||||||||||||
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#3: Chemical | ChemComp-LFA / #4: Chemical | ChemComp-OLC / ( | #5: Chemical | #6: Chemical | ChemComp-HEX / #7: Chemical | #8: Chemical | ChemComp-AR / #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.16 Å3/Da / Density % sol: 43.06 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 3.0 M Ammonium Sulfate,0.1 M Sodium Acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97241 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97241 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 57738 / % possible obs: 99 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 16.29 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 4476 / CC1/2: 0.34 / Rrim(I) all: 1.769 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XXJ Resolution: 1.65→83.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.872 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / 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: 27.514 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→83.02 Å
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Refine LS restraints |
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