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- PDB-7avn: 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: 7avn | ||||||||||||
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Title | Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1 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 | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.9 MB | Display | ![]() |
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Full document | ![]() | 5.9 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7avoC ![]() 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 | #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: 47.85 % |
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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: 1.6→50.98 Å / Num. obs: 59048 / % possible obs: 99.7 % / Redundancy: 10.9 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 23.2 / Num. measured all: 641326 / Scaling rejects: 13 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.892 / Num. unique obs: 2944 / CC1/2: 0.772 / Rpim(I) all: 0.284 / Rrim(I) all: 0.937 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JSI Resolution: 1.6→50.57 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.806 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / 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: 87.47 Å2 / Biso mean: 27.59 Å2 / Biso min: 11.75 Å2
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Refinement step | Cycle: final / Resolution: 1.6→50.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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