[English] 日本語
Yorodumi- PDB-6oh4: X-ray crystal structure of the mouse CMP-sialic acid transporter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oh4 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of the mouse CMP-sialic acid transporter in complex with CMP, by hanging drop vapor diffusion | ||||||
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 / MIRAS / Resolution: 3.38 Å | ||||||
Authors | Ahuja, S. / Whorton, M.R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Elife / Year: 2019 Title: Structural basis for mammalian nucleotide sugar transport. Authors: Ahuja, S. / Whorton, M.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6oh4.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6oh4.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 6oh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oh4_validation.pdf.gz | 814.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6oh4_full_validation.pdf.gz | 824.9 KB | Display | |
Data in XML | 6oh4_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6oh4_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/6oh4 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/6oh4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 15 - 317 / Label seq-ID: 15 - 317
| ||||||||||||||||||
Details | The authors state that there are no biologically relevant macromolecular assemblies in this structure. |
-Components
#1: Protein | Mass: 37494.902 Da / Num. of mol.: 2 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 #2: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.36 Å3/Da / Density % sol: 71.78 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25.6-26.8% PEG 400, 0.1 M Tris pH 8.5, and 0.1 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03313 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03313 Å / Relative weight: 1 |
Reflection | Resolution: 3.38→49 Å / Num. obs: 11456 / % possible obs: 67.3 % / Redundancy: 3.6 % / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.38→3.5 Å / Num. unique obs: 51 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 3.38→49 Å / Cor.coef. Fo:Fc: 0.761 / Cor.coef. Fo:Fc free: 0.691 / SU B: 53.451 / SU ML: 0.765 / Cross valid method: THROUGHOUT / ESU R Free: 0.79 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 143.981 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.38→49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|