+Open data
-Basic information
Entry | Database: PDB / ID: 5ax7 | ||||||
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Title | yeast pyruvyltransferase Pvg1p | ||||||
Components | Pyruvyl transferase 1 | ||||||
Keywords | TRANSFERASE / pyruvylation | ||||||
Function / homology | Function and homology information pyruvyltransferase activity / 4,6-pyruvylated galactose residue biosynthetic process / fungal-type cell wall biogenesis / Transferases / cell wall organization / Golgi apparatus / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å | ||||||
Authors | Kanekiyo, M. / Yoritsune, K. / Yoshinaga, S. / Higuchi, Y. / Takegawa, K. / Kakuta, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: A rationally engineered yeast pyruvyltransferase Pvg1p introduces sialylation-like properties in neo-human-type complex oligosaccharide Authors: Higuchi, Y. / Yoshinaga, S. / Yoritsune, K. / Tateno, H. / Hirabayashi, J. / Nakakita, S. / Kanekiyo, M. / Kakuta, Y. / Takegawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ax7.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ax7.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ax7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ax7_validation.pdf.gz | 409.1 KB | Display | wwPDB validaton report |
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Full document | 5ax7_full_validation.pdf.gz | 411.4 KB | Display | |
Data in XML | 5ax7_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5ax7_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5ax7 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5ax7 | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 39105.719 Da / Num. of mol.: 2 / Fragment: UNP residues 54-401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: pvg1, SPAC8F11.10c, SPACUNK4.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT27, Transferases #2: Chemical | ChemComp-ZN / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 293.4 K / Method: vapor diffusion, sitting drop Details: 200 mM magnesium choloride, 10 mM zinc chloride, 26% (w/v) Poly(acrylic acid sodium salt) 5100 in 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.3 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.46→10.99 Å / Num. obs: 55667 / % possible obs: 99.8 % / Redundancy: 5.77 % / Net I/σ(I): 25.14 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.46→10.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.868 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.694 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→10.99 Å
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Refine LS restraints |
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