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- PDB-3zy3: Crystal structure of POFUT1 in complex with GDP (crystal-form-III) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zy3 | ||||||
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Title | Crystal structure of POFUT1 in complex with GDP (crystal-form-III) | ||||||
![]() | PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1 | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / GT-B / CATALYTIC MECHANISM / GT65 | ||||||
Function / homology | ![]() peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / fucose metabolic process / protein O-linked glycosylation / Notch signaling pathway / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lira-Navarrete, E. / Valero-Gonzalez, J. / Villanueva, R. / Martinez-Julvez, M. / Tejero, T. / Merino, P. / Panjikar, S. / Hurtado-Guerrero, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.8 KB | Display | ![]() |
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PDB format | ![]() | 245.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zy2SC ![]() 3zy4C ![]() 3zy5C ![]() 3zy6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.447, 0.4476, 0.7745), |
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Components
#1: Protein | Mass: 41008.746 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.72 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / 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: 1.86→24.98 Å / Num. obs: 64057 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.1 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZY2 Resolution: 1.86→114.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.706 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.142 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.202 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→114.47 Å
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Refine LS restraints |
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