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Yorodumi- PDB-3zy2: Crystal structure of POFUT1 in complex with GDP (High resolution ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zy2 | ||||||
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Title | Crystal structure of POFUT1 in complex with GDP (High resolution dataset) | ||||||
Components | PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / GT-B / CATALYTIC MECHANISM / GT65 | ||||||
Function / homology | Function and homology information fucosyltransferase activity / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucose metabolic process / protein O-linked glycosylation / Notch signaling pathway / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | CAENORHABDITIS ELEGANS (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å | ||||||
Authors | Lira-Navarrete, E. / Valero-Gonzalez, J. / Villanueva, R. / Martinez-Julvez, M. / Tejero, T. / Merino, P. / Panjikar, S. / Hurtado-Guerrero, R. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural Insights Into the Mechanism of Protein O-Fucosylation. Authors: Lira-Navarrete, E. / Valero-Gonzalez, J. / Villanueva, R. / Martinez-Julvez, M. / Tejero, T. / Merino, P. / Panjikar, S. / Hurtado-Guerrero, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zy2.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zy2.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zy2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3zy2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3zy2_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3zy2_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/3zy2 ftp://data.pdbj.org/pub/pdb/validation_reports/zy/3zy2 | 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: 41008.746 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 / References: UniProt: Q18014, peptide-O-fucosyltransferase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % Description: 3ZY2 WAS SOLVED FROM SAD PHASING METHODOLOGY USING A HIGHLY REDUNDANT DATASET TOGETHER WITH AN ISOMORPHOUS HIGH RESOLUTION DATASET (IN THIS CASE THIS ISOMORPHOUS HIGH RESOLUTION DATASET IS 3ZY2) |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.99 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→19.5 Å / Num. obs: 53812 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.54→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.54→70.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.307 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.687 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→70.63 Å
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Refine LS restraints |
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