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Yorodumi- PDB-6oh3: X-ray crystal structure of the mouse CMP-sialic acid transporter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oh3 | ||||||
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Title | X-ray crystal structure of the mouse CMP-sialic acid transporter in complex with CMP-sialic acid, by lipidic cubic phase | ||||||
Components | CMP-sialic acid transporter | ||||||
Keywords | TRANSPORT PROTEIN / drug/metabolite transporter / nucleotide-sugar / sialic acid / glycosylation | ||||||
Function / homology | Function and homology information CMP-N-acetylneuraminate transmembrane transporter activity / CMP-N-acetylneuraminate transmembrane transport / Transport of nucleotide sugars / Sialic acid metabolism / antiporter activity / Golgi membrane / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ahuja, S. / Whorton, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2019 Title: Structural basis for mammalian nucleotide sugar transport. Authors: Ahuja, S. / Whorton, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oh3.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oh3.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 6oh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oh3_validation.pdf.gz | 735.8 KB | Display | wwPDB validaton report |
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Full document | 6oh3_full_validation.pdf.gz | 737.8 KB | Display | |
Data in XML | 6oh3_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 6oh3_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6oh3 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6oh3 | HTTPS FTP |
-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: 35852.055 Da / Num. of mol.: 1 / Fragment: residues 1-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc35a1 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: Q61420 |
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#2: Chemical | ChemComp-NCC / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase Details: 28.05% PEG 350 MME, 40 mM Tris pH 8.0, and 40 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→48 Å / Num. obs: 8305 / % possible obs: 99.8 % / Redundancy: 4.1 % / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.75→2.85 Å / Num. unique obs: 561 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.924 / SU B: 27.572 / SU ML: 0.47 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.613 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→48 Å
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Refine LS restraints |
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