+Open data
-Basic information
Entry | Database: PDB / ID: 3lw6 | ||||||
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Title | Crystal Structure of Drosophila beta1,4-galactosyltransferase-7 | ||||||
Components | Beta-4-galactosyltransferase 7 | ||||||
Keywords | TRANSFERASE / Protein-Mn-UDP complex / Glycosyltransferase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Ramakrishnan, B. / Qasba, P.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structure of the catalytic domain of Drosophila beta1,4-Galactosyltransferase-7. Authors: 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 | 3lw6.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lw6.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/3lw6 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lw6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | monomer |
-Components
#1: Protein | Mass: 33320.293 Da / Num. of mol.: 1 / Fragment: Catalytic domain Mutation: N-terminal residues 1 to 70 and the C-terminal residues 312 to 322 were deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: 4-galactosyltransferase-7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, 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-UDP / |
#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-MN / |
#5: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 10-20 mg/ml protein with 33 mm UDP and 66 mM MnCl2 with a precipitation solution containing 100 mM Tris.HCl, 1 M NaCl, 15% MPD and 5% PEG 4K., pH 8.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2009 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. all: 41321 / Num. obs: 41321 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.9 % / Rsym value: 0.063 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1669 / Rsym value: 0.413 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Brominated structure was solved using SAD at 2.0 A resolution and the cordinated are used as the stating model. Resolution: 1.81→36.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.81→36.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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