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Yorodumi- PDB-4m4k: Crystal structure of the Drosphila beta,14galactosyltransferase 7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m4k | |||||||||
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Title | Crystal structure of the Drosphila beta,14galactosyltransferase 7 mutant D211N complex with manganese, UDP-Gal and xylobiose | |||||||||
Components | Beta-4-galactosyltransferase 7 | |||||||||
Keywords | TRANSFERASE / GT-A glycosyltransferase family / UDP-Gal and Xylose / 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 Placement / Resolution: 2.2 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 | 4m4k.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m4k.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 4m4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m4k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4m4k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4m4k_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4m4k_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m4k ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m4k | HTTPS FTP |
-Related structure data
Related structure data | 4irpC 4irqC 4lw3C 4lw6SC 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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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 33319.305 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311 / Mutation: D211N Source method: isolated from a genetically manipulated source Details: expressed as inclusion bodies and in vitro refolded Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: 4galactosyltransferase 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: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
-Non-polymers , 4 types, 177 molecules
#3: Chemical | ChemComp-MN / | ||
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#4: Chemical | ChemComp-GDU / | ||
#5: Chemical | #6: 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 6000, 10% MPD, 1M NaCl, 10 mM MnCl2, 10 mM UDP-Gal and 10 mM xylobiose, 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 28, 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: 2.2→50 Å / Num. all: 24123 / Num. obs: 23650 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 9.6 % / Rsym value: 0.077 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2345 / Rsym value: 0.66 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular Placement Starting model: PDB entry 4LW6 Resolution: 2.2→36.976 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.32 / 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: 2.2→36.976 Å
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Refine LS restraints |
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LS refinement shell |
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