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Yorodumi- PDB-4lds: The inward-facing structure of the glucose transporter from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lds | ||||||
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Title | The inward-facing structure of the glucose transporter from Staphylococcus epidermidis | ||||||
Components | Glucose transporter GlcP | ||||||
Keywords | transport protein / membrane protein / alpha helical transmembrane protein / glucose transporter / major facilitator superfamily | ||||||
Function / homology | Function and homology information symporter activity / carbohydrate transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Choe, J. / Aleshin, A. / Iancu, C.V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal structure of a glucose/H+ symporter and its mechanism of action. Authors: Iancu, C.V. / Zamoon, J. / Woo, S.B. / Aleshin, A. / Choe, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lds.cif.gz | 317.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lds.ent.gz | 265 KB | Display | PDB format |
PDBx/mmJSON format | 4lds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/4lds ftp://data.pdbj.org/pub/pdb/validation_reports/ld/4lds | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 48407.477 Da / Num. of mol.: 2 / Fragment: unp residues 22-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200) (bacteria) Strain: ATCC 12228 / FDA PCI 1200 / Gene: glcP, SE_0247 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2VG78 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.29 Å3/Da / Density % sol: 80.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24% PEG 400, 0.1 M Ca Acetate, 0.1 M NaCl, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.8211 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8211 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. all: 39873 / Num. obs: 38767 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 50.95 Å2 / Rsym value: 0.117 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2683 / Rsym value: 0.598 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→19.902 Å / SU ML: 0.59 / σ(F): 2.36 / Phase error: 38.19 / Stereochemistry target values: LS_WUNIT_K1
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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: 3.2→19.902 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: -36.4923 Å / Origin y: 56.8719 Å / Origin z: -11.196 Å
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Refinement TLS group | Selection details: all |