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Yorodumi- PDB-7avp: Structure of marine actinobacteria clade rhodopsin (MacR) in viol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7avp | ||||||||||||
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Title | Structure of marine actinobacteria clade rhodopsin (MacR) in violet form | ||||||||||||
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 / Bacteriorhodopsin Function and homology information | ||||||||||||
Biological species | Candidatus Actinomarina minuta (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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 | 7avp.cif.gz | 193.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7avp.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 7avp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7avp_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7avp_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7avp_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 7avp_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7avp ftp://data.pdbj.org/pub/pdb/validation_reports/av/7avp | HTTPS FTP |
-Related structure data
Related structure data | 7avnC 7avoC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24544.504 Da / Num. of mol.: 1 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 | ||||
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#2: Chemical | ChemComp-LFA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 10% PEG 6000 140 mM NaCl 0.1M NaAcetate 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: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.076→59.241 Å / Num. obs: 71975 / % possible obs: 89.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 10.28 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.024 / Net I/σ(I): 13.74 |
Reflection shell | Resolution: 1.076→1.181 Å / Mean I/σ(I) obs: 1.91 / Num. unique obs: 3599 / CC1/2: 0.7472 / Rpim(I) all: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JSI Resolution: 1.09→59.24 Å / SU ML: 0.0625 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3501 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→59.24 Å
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Refine LS restraints |
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LS refinement shell |
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