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Yorodumi- PDB-1pzy: W314A-BETA1,4-GALACTOSYLTRANSFERASE-I COMPLEXED WITH ALPHA-LACTAL... -
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-Basic information
Entry | Database: PDB / ID: 1pzy | ||||||
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Title | W314A-BETA1,4-GALACTOSYLTRANSFERASE-I COMPLEXED WITH ALPHA-LACTALBUMIN IN THE PRESENCE OF N-ACETYLGLUCOSAMINE, UDP AND MANGANESE | ||||||
Components |
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Keywords | TRANSFERASE ACTIVATOR/TRANSFERASE / Beta1 / 4-Galactosyltransferase-I Tryptophan Mutant / Flexible loop Conformation / Protease Digetion / Substrate Binding / Catalytic Mechanism / TRANSFERASE ACTIVATOR-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information Lactose synthesis / 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 ...Lactose synthesis / 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 / regulation of acrosome reaction / penetration of zona pellucida / Golgi trans cisterna / lactose synthase activity / macrophage migration / lactose biosynthetic process / oligosaccharide biosynthetic process / development of secondary sexual characteristics / desmosome / acute inflammatory response / positive regulation of epithelial cell proliferation involved in wound healing / galactose metabolic process / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / epithelial cell development / alpha-tubulin binding / cytoskeletal protein binding / extracellular matrix organization / filopodium / epithelial cell proliferation / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / lysozyme activity / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / external side of plasma membrane / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Role of Tryptophan 314 in the Conformational Changes of beta 1,4-Galactosyltransferase-I Authors: Ramasamy, V. / 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 | 1pzy.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzy.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzy ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzy | HTTPS FTP |
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-Related structure data
Related structure data | 1pztC 1nmmS 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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Details | CHAINS A AND B FORM FIRST, C AND D FORMS SECOND LACTOSE SYNTHASE COMPLEX |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: REGULATORY SUBUNIT OF LACTOSE SYNTHASE Source method: isolated from a genetically manipulated source Details: CHAINS A AND B FORM FIRST, B AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET171 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29752 #2: Protein | Mass: 32734.449 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, residues 130-402 / Mutation: W314A, C342T Source method: isolated from a genetically manipulated source Details: CHAINS C AND D FORM FIRST, B AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) Bos taurus (cattle) Description: N-TERMINAL CARRIES A TAG CONTAINING 13 AMINO ACIDS 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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-Sugars , 1 types, 2 molecules
#4: Sugar |
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-Non-polymers , 4 types, 257 molecules
#3: Chemical | #5: Chemical | #6: Chemical | #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: 2.9 Å3/Da / Density % sol: 57.3 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 11% PEG 4000, 0.1M Sodium chloride and 0.1M Sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Aug 31, 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: 2.3→25 Å / Num. obs: 46294 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4427 / Rsym value: 0.48 / % possible all: 93.4 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. obs: 47881 / Num. measured all: 161993 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NMM Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.004 / 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: 33.1219 Å2 / ksol: 0.327069 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.44 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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