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Yorodumi- PDB-1tw1: beta-1,4-galactosyltransferase mutant Met344His (m344H-Gal-T1) co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tw1 | ||||||
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Title | beta-1,4-galactosyltransferase mutant Met344His (m344H-Gal-T1) complex with UDP-galactose and magnesium | ||||||
Components | Beta-1,4-galactosyltransferase 1 | ||||||
Keywords | TRANSFERASE / Met344His mutation / closed conformation / Mn 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 / brush border membrane / lipid metabolic process / 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 / SYNCHROTRON / 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 | 1tw1.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tw1.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/1tw1 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/1tw1 | HTTPS FTP |
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-Related structure data
Related structure data | 1tvyC 1tw5C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 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 |
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-Non-polymers , 6 types, 534 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-MES / | #7: 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: 2.29 Å3/Da / Density % sol: 45.9 % |
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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: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9807 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2003 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9807 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 29702 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.072 |
Reflection shell | Resolution: 2.3→2.38 Å / Rsym value: 0.47 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O0r Resolution: 2.3→37.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1680493.85 / 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: 60.5576 Å2 / ksol: 0.341572 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→37.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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