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Yorodumi- PDB-9g11: sugar/H+ symporter STP6 in inward occluded conformation with gluc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9g11 | ||||||
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Title | sugar/H+ symporter STP6 in inward occluded conformation with glucose bound | ||||||
Components | Sugar transport protein 6 | ||||||
Keywords | MEMBRANE PROTEIN / Sugar transporter / STP / MFS | ||||||
Function / homology | Function and homology information monosaccharide transmembrane transporter activity / carbohydrate transmembrane transport / symporter activity / membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Andersen, C.G. / Bavnhoj, L. / Pedersen, B.P. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Comparative biochemical analysis of the plant sugar transporters STP6 and STP10 Authors: Andersen, C.G. / Bavnhoj, L. / Driller, J.H. / Brag, S. / Pedersen, B.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9g11.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9g11.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 9g11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/9g11 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/9g11 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55951.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: STP6, At3g05960, F2O10.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9SFG0 | ||
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#2: Sugar | ChemComp-BGC / | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.05 % / Description: Rods |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG smear (PEG2000, PEG3000, PEG3500, PEG4000, PEG5000), 0.1M Hepes pH 8.0, 0.4M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→84.23 Å / Num. obs: 19456 / % possible obs: 96.5 % / Redundancy: 4.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.123 / Rrim(I) all: 0.258 / Χ2: 0.99 / Net I/σ(I): 7.3 / Num. measured all: 80631 |
Reflection shell | Resolution: 3.2→3.42 Å / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.168 / Num. measured all: 15369 / Num. unique obs: 3591 / CC1/2: 0.347 / Rpim(I) all: 0.627 / Rrim(I) all: 1.33 / Χ2: 1 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→84.23 Å / Cross valid method: FREE R-VALUE / σ(F): 232.13 / Phase error: 25.5348 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 69.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→84.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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