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Yorodumi- PDB-5ogk: Crystal structure of a nucleotide sugar transporter with bound nu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogk | ||||||
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Title | Crystal structure of a nucleotide sugar transporter with bound nucleotide sugar. | ||||||
Components | GDP-mannose transporter 1 | ||||||
Keywords | MEMBRANE PROTEIN / SLC35 / Golgi transporter / nucleotide-sugar | ||||||
Function / homology | Function and homology information GDP-mannose transmembrane transporter activity / GDP-mannose transmembrane transport / antiporter activity / cytoplasmic vesicle membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Newstead, S. / Parker, J.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2017 Title: Structural basis of nucleotide sugar transport across the Golgi membrane. Authors: Parker, J.L. / Newstead, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ogk.cif.gz | 471.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogk.ent.gz | 391.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ogk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ogk_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5ogk_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5ogk_validation.xml.gz | 94.6 KB | Display | |
Data in CIF | 5ogk_validation.cif.gz | 122.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogk ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogk | HTTPS FTP |
-Related structure data
Related structure data | 5ogeSC 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37044.504 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VRG4, GOG5, LDB3, MCD3, VAN2, VIG4, YGL225W / Production host: Saccharomyces (fungus) / Strain (production host): BJ5460 / References: UniProt: P40107 #2: Chemical | #3: Chemical | ChemComp-OLC / ( |
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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: 2.8 Å3/Da / Density % sol: 56.11 % / Description: 30 x 5 uM |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 5 Details: 26 - 30 % (v/v) PEG 400, 0.1 M sodium citrate pH 5.0 and 75 mM sodium chloride or sodium acetate. GDP-mannose was soaked in at 20mM overnight. |
-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→45.3 Å / Num. obs: 36110 / % possible obs: 96.8 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rpim(I) all: 0.2 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 3.6→3.76 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4518 / CC1/2: 0.3 / Rpim(I) all: 1.11 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OGE Resolution: 3.6→44.328 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.52 / 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: 3.6→44.328 Å
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Refine LS restraints |
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LS refinement shell |
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