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Yorodumi- PDB-3o7p: Crystal structure of the E.coli Fucose:proton symporter, FucP (N162A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o7p | ||||||
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Title | Crystal structure of the E.coli Fucose:proton symporter, FucP (N162A) | ||||||
Components | L-fucose-proton symporter | ||||||
Keywords | TRANSPORT PROTEIN / L-Fucose / symporter / Multi-pass membrane protein / transporter | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.196 Å | ||||||
Authors | Dang, S.Y. / Sun, L.F. / 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 | 3o7p.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o7p.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o7p ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7p | HTTPS FTP |
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-Related structure data
Related structure data | 3o7qSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 47531.547 Da / Num. of mol.: 1 / Mutation: N162A 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: 4.28 Å3/Da / Density % sol: 71.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 34% PEG 400, 0.1M cacodylate, 0.1M MgCl2, 0.05M NaF, 0.2M KCl, 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: SSRF / Beamline: BL17U / Wavelength: 0.90922 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2010 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90922 Å / Relative weight: 1 |
Reflection | Resolution: 3.196→36.302 Å / Num. obs: 13809 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O7Q Resolution: 3.196→36.302 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 26.12 / 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: 83.376 Å2 / ksol: 0.308 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.196→36.302 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: 89.8084 Å / Origin y: 52.3711 Å / Origin z: -40.1235 Å
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Refinement TLS group | Selection details: chain A |