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Yorodumi- PDB-4lw3: Crystal structure of the Drosophila beta1,4galactosyltransferase7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lw3 | ||||||
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Title | Crystal structure of the Drosophila beta1,4galactosyltransferase7 catalytic domain D211N single mutant enzyme complex with manganese and UDP-galactose | ||||||
Components | Beta-4-galactosyltransferase 7 | ||||||
Keywords | TRANSFERASE / GT-A glycosyltransferase family / manganese and UDp-galactose / Golgi | ||||||
Function / homology | Function and homology information xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosylation / proteoglycan biosynthetic process / N-glycan processing / protein glycosylation / carbohydrate metabolic process / Golgi membrane / nucleotide binding ...xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosylation / proteoglycan biosynthetic process / N-glycan processing / protein glycosylation / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | 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 | 4lw3.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lw3.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lw3_validation.pdf.gz | 819.8 KB | Display | wwPDB validaton report |
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Full document | 4lw3_full_validation.pdf.gz | 822.2 KB | Display | |
Data in XML | 4lw3_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 4lw3_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lw3 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lw3 | HTTPS FTP |
-Related structure data
Related structure data | 4irpC 4irqC 4lw6C 4m4kC 3lw6S S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33319.305 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311 / Mutation: D221N Source method: isolated from a genetically manipulated source Details: Protein expressed as inclusion bodies and in vitro refolded Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: 4-galactosyltransferase-7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780 Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9VBZ9, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-galactosyltransferase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-GDU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.52 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM HEPES, 5% PEG 6K, 10% MPD, 2 mM MnCl2, 2 mM UDP-Gal, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-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: Jul 17, 2013 / 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→50 Å / Num. obs: 29731 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rsym value: 0.057 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2614 / Rsym value: 0.353 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LW6 Resolution: 2→28.913 Å / SU ML: 0.2 / Cross valid method: Throught / σ(F): 1.33 / Phase error: 22.77 / 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→28.913 Å
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Refine LS restraints |
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LS refinement shell |
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