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Yorodumi- PDB-1nmm: beta-1,4-galactosyltransferase mutant Cys342Thr complex with alph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nmm | |||||||||
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Title | beta-1,4-galactosyltransferase mutant Cys342Thr complex with alpha-lactalbumin and GlcNAc | |||||||||
Components |
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Keywords | TRANSFERASE ACTIVATOR/TRANSFERASE / beta1 / 4-galactosyltransferase / Cys342Thr mutation / alpha-lactalbumin complex / 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 / 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 Å | |||||||||
Authors | Ramakrishnan, B. / Shah, P.S. / Qasba, P.K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: alpha-Lactalbumin (LA) stimulates milk beta-1,4-galactosyltransferase I (beta 4Gal-T1) to transfer glucose from UDP-glucose to N-acetylglucosamine. Crystal structure of beta 4Gal-T1 x LA complex with UDP-Glc. Authors: Ramakrishnan, B. / Shah, P.S. / 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 | 1nmm.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmm.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmm_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
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Full document | 1nmm_full_validation.pdf.gz | 503.3 KB | Display | |
Data in XML | 1nmm_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 1nmm_validation.cif.gz | 59.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmm ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-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, C AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) Mus musculus (house mouse) / Variant: BL21 / Plasmid: pET17.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29752 #2: Protein | Mass: 32849.578 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, residues 130-402 Source method: isolated from a genetically manipulated source Details: CHAINS A AND B FORM FIRST, C AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) Bos taurus (cattle) / Variant: B834 / Plasmid: pET23c / Production host: Escherichia coli (E. coli) 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 , 3 types, 786 molecules
#3: Chemical | #5: Chemical | #6: 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: 2.65 Å3/Da / Density % sol: 53.1 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, Sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, 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: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2000 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 71567 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.079 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique all: 6974 / Rsym value: 0.53 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 265383 / Rmerge(I) obs: 0.079 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.72 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.4289 Å2 / ksol: 0.332233 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 69391 / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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