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Yorodumi- PDB-4irq: Crystal structure of catalytic domain of human beta1,4galactosylt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4irq | ||||||
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Title | Crystal structure of catalytic domain of human beta1,4galactosyltransferase 7 in closed conformation in complex with manganese and UDP | ||||||
Components | Beta-1,4-galactosyltransferase 7 | ||||||
Keywords | TRANSFERASE / GT-A fold / closed conformation / manganese and UDP complex / glycosyltransferase / Golgi | ||||||
Function / homology | Function and homology information xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / glycosylation / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / proteoglycan metabolic process ...xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / glycosylation / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / proteoglycan metabolic process / glycosaminoglycan metabolic process / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / supramolecular fiber organization / negative regulation of fibroblast proliferation / protein modification process / manganese ion binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal structures of beta-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding. Authors: Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4irq.cif.gz | 221.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4irq.ent.gz | 176.5 KB | Display | PDB format |
PDBx/mmJSON format | 4irq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4irq_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4irq_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4irq_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 4irq_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4irq ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4irq | HTTPS FTP |
-Related structure data
Related structure data | 4irpC 4lw3C 4lw6C 4m4kC 3lw6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29216.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: human Galectin-1 as fusion protein / Source: (gene. exp.) Homo sapiens (human) Gene: 4galactosyltransferase, B4GALT7, beta1, UNQ748/PRO1478, XGALT1 Plasmid: PET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9UBV7, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-galactosyltransferase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-UDP / #4: Chemical | ChemComp-TRS / #5: 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: 3.38 Å3/Da / Density % sol: 63.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tri.HCl, pH 8.5, 8% PEG 8000 as precipitating agent, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2012 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 66815 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 0.091 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 5725 / Rsym value: 0.523 / % possible all: 83.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LW6 Resolution: 2.3→37.847 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→37.847 Å
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Refine LS restraints |
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LS refinement shell |
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