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Yorodumi- PDB-7avo: Structure of marine actinobacteria clade rhodopsin (MacR) in oran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7avo | ||||||||||||
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Title | Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1211 space group | ||||||||||||
Components | Bacteriorhodopsin | ||||||||||||
Keywords | MEMBRANE PROTEIN / retinal / rhodopsin / bacteriorhodopsin / proton pump / ion transport | ||||||||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Bacteriorhodopsin Function and homology information | ||||||||||||
Biological species | Candidatus Actinomarina minuta (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Gushchin, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gordeliy, V. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: To Be Published Title: Alternating Access Mechanism in a Minimalistic Light-Driven Proton Pump Authors: Shevchenko, V. / Gushchin, I. / Polovinkin, V. / Kovalev, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7avo.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7avo.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 7avo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7avo ftp://data.pdbj.org/pub/pdb/validation_reports/av/7avo | HTTPS FTP |
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-Related structure data
Related structure data | 7avnC 7avpC 5jsiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24544.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5DM51 #2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-OLB / ( | #4: Chemical | ChemComp-OLC / ( | #5: Water | ChemComp-HOH / | 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: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 1.0 M NH4SO4, 0.1 M NaOAc pH 5.2 |
-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-F / Detector: PIXEL / Date: Dec 13, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97241 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→48.94 Å / Num. obs: 48957 / % possible obs: 98 % / Redundancy: 14.5 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Net I/σ(I): 25.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JSI Resolution: 1.7→48.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.726 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 95.29 Å2 / Biso mean: 28.564 Å2 / Biso min: 12.28 Å2
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Refinement step | Cycle: final / Resolution: 1.7→48.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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