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- PDB-7avo: Structure of marine actinobacteria clade rhodopsin (MacR) in oran... -
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Open data
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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 | ||||||||||||
![]() | Bacteriorhodopsin | ||||||||||||
![]() | 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![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gushchin, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gordeliy, V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.7 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7avnC ![]() 7avpC ![]() 5jsiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() Production host: ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure: ![]() 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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