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Yorodumi- PDB-7znd: Crystal structure of the light-driven inward proton pump xenorhod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7znd | ||||||
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Title | Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 7.6 in the absence of sodium at 100K | ||||||
Components | xenorhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / retinal / rhodopsin / xenorhodopsin / ion transport / isomerization / photocycle | ||||||
Function / homology | EICOSANE / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION Function and homology information | ||||||
Biological species | Bacillus coahuilensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.985 Å | ||||||
Authors | Kovalev, K. / Tsybrov, F. / Alekseev, A. / Bourenkov, G. / Gordeliy, V. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 Title: Mechanisms of inward transmembrane proton translocation. Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / ...Authors: Kovalev, K. / Tsybrov, F. / Alekseev, A. / Shevchenko, V. / Soloviov, D. / Siletsky, S. / Bourenkov, G. / Agthe, M. / Nikolova, M. / von Stetten, D. / Astashkin, R. / Bukhdruker, S. / Chizhov, I. / Royant, A. / Kuzmin, A. / Gushchin, I. / Rosselli, R. / Rodriguez-Valera, F. / Ilyinskiy, N. / Rogachev, A. / Borshchevskiy, V. / Schneider, T.R. / Bamberg, E. / Gordeliy, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7znd.cif.gz | 168.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7znd.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 7znd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7znd_validation.pdf.gz | 7.9 MB | Display | wwPDB validaton report |
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Full document | 7znd_full_validation.pdf.gz | 7.8 MB | Display | |
Data in XML | 7znd_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 7znd_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7znd ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7znd | HTTPS FTP |
-Related structure data
Related structure data | 7zmyC 7zn0C 7zn3C 7zn8C 7zn9C 7znaC 7znbC 7zncC 7zneC 7zngC 7znhC 7zniC 1xioS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: FME / Beg label comp-ID: FME / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 25725.627 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus coahuilensis (bacteria) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 142 molecules
#2: Chemical | ChemComp-LFA / #3: Chemical | ChemComp-OLA / #4: Chemical | ChemComp-OLC / ( #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-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: 2.92 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 1.2 M Ammonium phosphate pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.985→59.792 Å / Num. obs: 42397 / % possible obs: 90.2 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.985→2.168 Å / Rmerge(I) obs: 1.636 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2567 / CC1/2: 0.441 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XIO Resolution: 1.985→20 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.868 / SU B: 7.67 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.362 / ESU R Free: 0.255 / 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: 127.24 Å2 / Biso mean: 33.37 Å2 / Biso min: 12.1 Å2
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Refinement step | Cycle: final / Resolution: 1.985→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.985→2.035 Å / Rfactor Rfree error: 0
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