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Yorodumi- PDB-6xbo: X-ray crystal structure of the mouse CMP-Sialic acid transporter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xbo | ||||||
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Title | X-ray crystal structure of the mouse CMP-Sialic acid transporter in complex with 5-methyl CMP | ||||||
Components | CMP-sialic acid transporter | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / glycobiology / sialic acid / 5-methyl CMP | ||||||
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 / carbohydrate transport / Golgi membrane / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ahuja, S. / Whorton, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos One / Year: 2021 Title: Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP. Authors: Ahuja, S. / Cahill, J. / Hartfield, K. / 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 | 6xbo.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xbo.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xbo ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xbo | HTTPS FTP |
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-Related structure data
Related structure data | 6oh2S S: Starting model for refinement |
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Similar 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc35a1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q61420 | ||||||
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#2: Chemical | ChemComp-5MC / | ||||||
#3: Chemical | ChemComp-OLC / ( #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / Details: 26.7-30% PEG 300, 0.1 M MES pH 6.5, and 0.1 M 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-D / Wavelength: 1.03319 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48 Å / Num. obs: 31213 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.06 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique obs: 2821 / CC1/2: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OH2 Resolution: 1.8→46.149 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.62 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.55 Å2 / Biso mean: 42.8349 Å2 / Biso min: 25.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→46.149 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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