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Yorodumi- PDB-3x3b: Crystal structure of the light-driven sodium pump KR2 in acidic state -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x3b | ||||||
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Title | Crystal structure of the light-driven sodium pump KR2 in acidic state | ||||||
Components | Sodium pumping rhodopsin | ||||||
Keywords | MEMBRANE PROTEIN / light-driven sodium pump | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dokdonia eikasta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Ishizuka, T. / Hoque, M.R. / Hososhima, S. / Kunitomo, H. ...Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Ishizuka, T. / Hoque, M.R. / Hososhima, S. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, M. / Nishizawa, T. / Taniguchi, R. / Kogure, K. / Maturana, A.D. / Iino, Y. / Yawo, H. / Ishitani, R. / Kandori, H. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump Authors: Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Hososhima, S. / Ishizuka, T. / Hoque, M.R. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, ...Authors: Kato, H.E. / Inoue, K. / Abe-Yoshizumi, R. / Kato, Y. / Ono, H. / Konno, M. / Hososhima, S. / Ishizuka, T. / Hoque, M.R. / Kunitomo, H. / Ito, J. / Yoshizawa, S. / Yamashita, K. / Takemoto, M. / Nishizawa, T. / Taniguchi, R. / Kogure, K. / Maturana, A.D. / Iino, Y. / Yawo, H. / Ishitani, R. / Kandori, H. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x3b.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x3b.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x3b ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x3b | HTTPS FTP |
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-Related structure data
Related structure data | 3x3cC 3ddlS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 32894.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dokdonia eikasta (bacteria) / Gene: NaR / Production host: Escherichia coli (E. coli) / References: UniProt: N0DKS8 | ||||
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#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.16 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4 Details: 42% PEG200, 0.1M sodium acetate pH 4.0, 0.05M MgCl2, lipidic cubic phase, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 16, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. all: 18137 / Num. obs: 17741 / % possible obs: 97.8 % | ||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DDL Resolution: 2.3→40.561 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 25.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.561 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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