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Yorodumi- PDB-4x5n: Crystal structure of SemiSWEET in the inward-open and outward-ope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x5n | ||||||
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Title | Crystal structure of SemiSWEET in the inward-open and outward-open conformations | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSPORT PROTEIN / SWEET / PQLC / membrane protein / sugar transporter | ||||||
Function / homology | Function and homology information sugar transmembrane transporter activity / carbohydrate transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli UMEA 3162-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lee, Y. / Nishizawa, T. / Yamashita, K. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter Authors: Lee, Y. / Nishizawa, T. / Yamashita, K. / Ishitani, R. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x5n.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x5n.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 4x5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x5n ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x5n | HTTPS FTP |
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-Related structure data
Related structure data | 4x5mSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11233.304 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli UMEA 3162-1 (bacteria) Gene: G925_04926 / Production host: Escherichia coli (E. coli) / References: UniProt: T8UDF6, UniProt: P0DMV3*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 23% PEG550MME, 100mM Tris-HCl (pH 8.0), 350mM NH4-citrate, 3% dimethyl sulfoxide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 9943 / % possible obs: 98 % / Redundancy: 3.3 % / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.3_1479) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X5M Resolution: 3→47.135 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→47.135 Å
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Refine LS restraints |
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LS refinement shell |
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