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Yorodumi- PDB-3mku: Structure of a Cation-bound Multidrug and Toxin Compound Extrusio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mku | ||||||
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Title | Structure of a Cation-bound Multidrug and Toxin Compound Extrusion (MATE) transporter | ||||||
Components | Multi antimicrobial extrusion protein (Na(+)/drug antiporter) MATE-like MDR efflux pump | ||||||
Keywords | TRANSPORT PROTEIN / MATE / multidrug transporter / cation-bound | ||||||
Function / homology | RUBIDIUM ION / : Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | He, X. / Szewczyk, P. / Karyakin, A. / Evin, M. / Hong, W.-X. / Zhang, Q. / Chang, G. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Structure of a cation-bound multidrug and toxic compound extrusion transporter. Authors: He, X. / Szewczyk, P. / Karyakin, A. / Evin, M. / Hong, W.X. / Zhang, Q. / Chang, G. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mku.cif.gz | 168.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mku.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/3mku ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mku | HTTPS FTP |
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-Related 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: 49761.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: NorM / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: C3NQD8 #2: Chemical | |
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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: 4.48 Å3/Da / Density % sol: 72.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 50mM Tris-HCl pH 7.2-8.6, 87 mM (NH4)2SO4, and 16-24% polyethylene glycol 250 dimethyl ether in D2O, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0093 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 4→20 Å / Num. obs: 13531 / Biso Wilson estimate: -12.2 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→20 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 2790903.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 12.1578 Å2 / ksol: 0.1 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 118.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 4.2→4.46 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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