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Yorodumi- PDB-1tw5: beta1,4-galactosyltransferase mutant M344H-Gal-T1 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tw5 | |||||||||
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Title | beta1,4-galactosyltransferase mutant M344H-Gal-T1 in complex with Chitobiose | |||||||||
Components | Beta-1,4-galactosyltransferase 1 | |||||||||
Keywords | TRANSFERASE / Met344His mutation / closed conformation / chitobiose binding | |||||||||
Function / homology | Function and homology information protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity ...protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / lipid metabolic process / brush border membrane / manganese ion binding / basolateral plasma membrane / external side of plasma membrane / Golgi apparatus / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Effect of the Met344His mutation on the conformational dynamics of bovine beta-1,4-galactosyltransferase: crystal structure of the Met344His mutant in complex with chitobiose Authors: Ramakrishnan, B. / Boeggeman, E. / 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 | 1tw5.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tw5.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tw5_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1tw5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1tw5_validation.xml.gz | 30 KB | Display | |
Data in CIF | 1tw5_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/1tw5 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/1tw5 | HTTPS FTP |
-Related structure data
Related structure data | 1tvyC 1tw1C 1o0rS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 5 molecules AB
#1: Protein | Mass: 32856.531 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: d129, Cys342Thr and Met344His Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) Description: N-terminal 13 amino acids belong to T7-tag from the vector Gene: B4GALT1 / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P08037, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 6 types, 507 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-MES / | #8: 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: 2.32 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Mes-NaOH, Ammonium sulfate, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 7, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / 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→40 Å / Num. obs: 34133 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.5 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O0R Resolution: 2.3→19.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1736275.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.8917 Å2 / ksol: 0.312053 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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