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Yorodumi- PDB-1oqm: A 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oqm | |||||||||
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Title | A 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltransferase in the presence of UDP-N-acetyl-galactosamine | |||||||||
Components |
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Keywords | TRANSFERASE / BIOSYNTHETIC PROTEIN / alpha-lactalbumin / beta1 / 4-galactosyltransferase / UDP-GalNAc | |||||||||
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 / 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 / lysozyme activity / manganese ion binding / basolateral plasma membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Ramakrishnan, B. / Qasba, P.K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure-based design of beta 1,4-galactosyltransferase I (beta 4Gal-T1) with equally efficient N-acetylgalactosaminyltransferase activity: point mutation broadens beta 4Gal-T1 donor specificity. Authors: Ramakrishnan, B. / Qasba, P.K. | |||||||||
History |
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Remark 999 | The N-terminal of chains B and D contains a 13 amino acid tag. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqm.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqm.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oqm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1oqm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1oqm_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 1oqm_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqm ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqm | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 | molecules A & B and C & D form a 1:1 complex between alpha-lactalbumin and beta1,4-galactosyltransferase |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: residues 21-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: LALBA / Plasmid: pET17.1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29752 #2: Protein | Mass: 32851.617 Da / Num. of mol.: 2 / Fragment: residues 57-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P08037, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase |
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-Non-polymers , 5 types, 637 molecules
#3: Chemical | #4: 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: 2.72 Å3/Da / Density % sol: 54.41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 5.5 Details: Sodium citrate, PEG4000, pH 5.5, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / 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: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2001 / 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: 2.1→20 Å / Num. all: 56163 / Num. obs: 56106 / % possible obs: 89.9 % / Observed criterion σ(I): 1 / Redundancy: 2.15 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.1→2.17 Å / Mean I/σ(I) obs: 2.01 / Num. unique all: 4719 / Rsym value: 0.359 / % possible all: 76 |
Reflection | *PLUS Num. obs: 62285 / % possible obs: 90 % / Num. measured all: 120498 / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.56 Å / Rfactor Rfree error: 0.003 / 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: 52.9573 Å2 / ksol: 0.327944 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 55765 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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