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Yorodumi- PDB-4n7x: The E254A mutant of the sodium bile acid symporter from Yersinia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n7x | ||||||
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Title | The E254A mutant of the sodium bile acid symporter from Yersinia frederiksenii | ||||||
Components | Transporter, sodium/bile acid symporter family | ||||||
Keywords | TRANSPORT PROTEIN / slc10 / sodium symport / bile acid / membrane protein / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS | ||||||
Function / homology | Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Up-down Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Yersinia frederiksenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Zhou, X. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structural basis of the alternating-access mechanism in a bile acid transporter. Authors: Zhou, X. / Levin, E.J. / Pan, Y. / McCoy, J.G. / Sharma, R. / Kloss, B. / Bruni, R. / Quick, M. / Zhou, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n7x.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n7x.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 4n7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n7x_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 4n7x_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 4n7x_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4n7x_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/4n7x ftp://data.pdbj.org/pub/pdb/validation_reports/n7/4n7x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33307.770 Da / Num. of mol.: 1 / Mutation: E254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: yfred0001_28600 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4ST46 |
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#2: 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 8.5 Details: 39% PEG 400, 100 mM Tris-HCL, 100 mM KCl, 20 mM MnCl2, 1-oleoyl-rac-glycerol, pH 8.5, Lipid Cubic Phase, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99991 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99991 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 12188 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 40.64 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.615 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.758 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.829 / SU ML: 0.18 / σ(F): 1.37 / Phase error: 23.3 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.98 Å2 / Biso mean: 42.3333 Å2 / Biso min: 21.34 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.758 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: 4
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