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Yorodumi- PDB-7xtl: Crystal structure of the C-terminal domain of human N-acetylgluco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xtl | ||||||
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Title | Crystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa | ||||||
Components | Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form | ||||||
Keywords | SUGAR BINDING PROTEIN / glycosyltransferase / N-glycan / N-glycosylation / Golgi / N-acetylglucosamine / carbohydrate-binding module / lectin | ||||||
Function / homology | Function and homology information alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity / glyoxylate metabolic process / N-Glycan antennae elongation / alanine-glyoxylate transaminase activity / acetylglucosaminyltransferase activity / N-glycan processing / Golgi stack / protein N-linked glycosylation / protein glycosylation ...alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity / glyoxylate metabolic process / N-Glycan antennae elongation / alanine-glyoxylate transaminase activity / acetylglucosaminyltransferase activity / N-glycan processing / Golgi stack / protein N-linked glycosylation / protein glycosylation / endoplasmic reticulum-Golgi intermediate compartment / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peroxisome / Maturation of spike protein / membrane => GO:0016020 / viral protein processing / endoplasmic reticulum lumen / Golgi membrane / endoplasmic reticulum / protein homodimerization activity / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å | ||||||
Authors | Miyazaki, T. / Oka, N. / Mori, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Glycobiology / Year: 2022 Title: Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family. Authors: Oka, N. / Mori, S. / Ikegaya, M. / Park, E.Y. / Miyazaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xtl.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xtl.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xtl_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 7xtl_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 7xtl_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7xtl_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtl ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtl | HTTPS FTP |
-Related structure data
Related structure data | 7xtmC 7xtnC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19263.764 Da / Num. of mol.: 2 / Fragment: CBM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: MGAT4A / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9UM21, alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium nitrate, 20%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→85.34 Å / Num. obs: 20101 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.06 / Rrim(I) all: 0.216 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 13 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2924 / CC1/2: 0.951 / Rpim(I) all: 0.234 / Rrim(I) all: 0.855 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2 model Resolution: 1.972→50.579 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.785 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.188 Details: Hydrogens have been added in their 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.557 Å2
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Refinement step | Cycle: LAST / Resolution: 1.972→50.579 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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