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Yorodumi- PDB-4wlm: Crystal structure of mouse Xyloside xylosyltransferase 1 complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wlm | ||||||
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Title | Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese | ||||||
Components | Xyloside xylosyltransferase 1 | ||||||
Keywords | TRANSFERASE / glycosyltransferase / manganese binding | ||||||
Function / homology | Function and homology information xylosyl alpha-1,3-xylosyltransferase / xylosyl alpha-1,3-xylosyltransferase activity / UDP-xylosyltransferase activity / O-glycan processing / manganese ion binding / endoplasmic reticulum membrane / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Yu, H. / Li, H. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Authors: Yu, H. / Takeuchi, M. / LeBarron, J. / Kantharia, J. / London, E. / Bakker, H. / Haltiwanger, R.S. / Li, H. / Takeuchi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wlm.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wlm.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/4wlm ftp://data.pdbj.org/pub/pdb/validation_reports/wl/4wlm | HTTPS FTP |
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-Related structure data
Related structure data | 4wlgC 4wlzC 4wm0C 4wmaC 4wmbC 4wmiC 4wmkC 4wn2C 4wmm 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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Unit cell |
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-Components
#1: Protein | Mass: 35295.500 Da / Num. of mol.: 2 / Fragment: unp residues 87-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xxylt1 / Production host: Homo sapiens (human) References: UniProt: Q3U4G3, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-SO4 / #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM HEPES, 1.5 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 14806 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 55.948 Å2
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Refinement step | Cycle: 1 / Resolution: 3→40 Å
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Refine LS restraints |
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