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Yorodumi- PDB-3o7q: Crystal structure of a Major Facilitator Superfamily (MFS) transp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o7q | ||||||
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Title | Crystal structure of a Major Facilitator Superfamily (MFS) transporter, FucP, in the outward conformation | ||||||
Components | L-fucose-proton symporter | ||||||
Keywords | TRANSPORT PROTEIN / L-Fucose / symporter / transporter / Multi-pass membrane protein | ||||||
Function / homology | Function and homology information galactose:proton symporter activity / arabinose:proton symporter activity / fucose:proton symporter activity / arabinose transmembrane transport / fucose transmembrane transport / galactose transmembrane transport / fucose metabolic process / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.143 Å | ||||||
Authors | Sun, L.F. / Dang, S.Y. / Wang, J. / Yan, N. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Structure of a fucose transporter in an outward-open conformation Authors: Dang, S.Y. / Sun, L.F. / Huang, Y. / Lu, F. / Liu, Y. / Gong, H. / Wang, J. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o7q.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o7q.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 3o7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o7q ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7q | HTTPS FTP |
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-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: 47574.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fucP, b2801, JW2772 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11551 |
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#2: Sugar | ChemComp-BNG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 71.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 34% PEG400, 0.1M cacodylate, 0.1M MgCl2, 0.05M NaF, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2009 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.143→35.643 Å / Num. obs: 14221 / % possible obs: 98.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.12 |
Reflection shell | Resolution: 3.14→3.25 Å / Rmerge(I) obs: 0.871 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.143→35.643 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 28.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.143→35.643 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 90.163 Å / Origin y: 52.5995 Å / Origin z: -39.6285 Å
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Refinement TLS group | Selection details: chain A |