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Yorodumi- PDB-4gbz: The structure of the MFS (major facilitator superfamily) proton:x... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gbz | ||||||
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Title | The structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to D-glucose | ||||||
Components | D-xylose-proton symporter | ||||||
Keywords | TRANSPORT PROTEIN / MFS / D-xylose:proton symporter | ||||||
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: 2.894 Å | ||||||
Authors | Sun, L.F. / Zeng, X. / Yan, C.Y. / Yan, N. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Authors: Sun, L. / Zeng, X. / Yan, C. / Sun, X. / Gong, X. / Rao, Y. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gbz.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gbz.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/4gbz ftp://data.pdbj.org/pub/pdb/validation_reports/gb/4gbz | 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: 53642.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xylE, b4031, JW3991 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGF4 | ||
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#2: Sugar | ChemComp-BGC / | ||
#3: Sugar | ChemComp-BNG / #4: 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: 3.55 Å3/Da / Density % sol: 65.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: 40 % (w/v) PEG400, 0.05 M Glycine pH 9.6 and 0.1 M LiCl , 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: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→40 Å / Num. all: 17911 / Num. obs: 17572 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.894→38.524 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 30.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.668 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.894→38.524 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: -20.195 Å / Origin y: 25.5829 Å / Origin z: -3.6462 Å
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Refinement TLS group | Selection details: all |