+Open data
-Basic information
Entry | Database: PDB / ID: 4qiq | ||||||
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Title | Crystal structure of D-xylose-proton symporter | ||||||
Components | D-xylose-proton symporter | ||||||
Keywords | TRANSPORT PROTEIN / MEMBRANE PROTEIN / MAJOR FACILITATOR SUPERFAMILY (MFS) / SUGAR TRANSPORTER / MEMBRANE | ||||||
Function / homology | Function and homology information D-xylose:proton symporter activity / D-xylose transmembrane transport / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å | ||||||
Authors | Wisedchaisri, G. / Park, M. / Iadanza, M.G. / Zheng, H. / Gonen, T. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE. Authors: Wisedchaisri, G. / Park, M.S. / Iadanza, M.G. / Zheng, H. / Gonen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qiq.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qiq.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qiq ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qiq | HTTPS FTP |
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-Related structure data
Related structure data | 4gbyS 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: 52186.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4031, JW3991, xylE / Plasmid: PET-15B/XYLEDNC / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P0AGF4 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 8.5% PEG8000, 0.1M MES PH 5.6, 0.1M ZINC ACETATE, 30MM D-GLUCOSE, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.127 / Wavelength: 1.127 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013 / Details: K-B FOCUSING MIRRORS |
Radiation | Monochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.1 |
Reflection | Resolution: 3.5→82 Å / Num. obs: 10580 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 208.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 5.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GBY Resolution: 3.51→29.65 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1.35 / Phase error: 37.04 / Stereochemistry target values: TWIN_LSQ_F
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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 mean: 79.47 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.51→29.65 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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