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Yorodumi- PDB-4mps: Crystal structure of rat Beta-galactoside alpha-2,6-sialyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mps | ||||||
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Title | Crystal structure of rat Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1), Northeast Structural Genomics Consortium Target RnR367A | ||||||
Components | Beta-galactoside alpha-2,6-sialyltransferase 1 | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / alpha-beta protein / Beta-galactoside alpha-2 / 6-sialyltransferase 1 | ||||||
Function / homology | Function and homology information beta-galactoside alpha-(2,6)-sialyltransferase / Sialic acid metabolism / N-Glycan antennae elongation / Termination of O-glycan biosynthesis / protein sialylation / beta-galactoside alpha-2,6-sialyltransferase activity / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Golgi trans cisterna ...beta-galactoside alpha-(2,6)-sialyltransferase / Sialic acid metabolism / N-Glycan antennae elongation / Termination of O-glycan biosynthesis / protein sialylation / beta-galactoside alpha-2,6-sialyltransferase activity / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Golgi trans cisterna / regulation of substrate adhesion-dependent cell spreading / negative regulation of chemotaxis / negative regulation of macrophage apoptotic process / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi cisterna membrane / protein glycosylation / Golgi medial cisterna / response to ethanol / membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Forouhar, F. / Meng, L. / Milaninia, S. / Seetharaman, J. / Su, M. / Kornhaber, G. / Montelione, G.T. / Hunt, J.F. / Moremen, K.W. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Enzymatic Basis for N-Glycan Sialylation: STRUCTURE OF RAT alpha 2,6-SIALYLTRANSFERASE (ST6GAL1) REVEALS CONSERVED AND UNIQUE FEATURES FOR GLYCAN SIALYLATION. Authors: Meng, L. / Forouhar, F. / Thieker, D. / Gao, Z. / Ramiah, A. / Moniz, H. / Xiang, Y. / Seetharaman, J. / Milaninia, S. / Su, M. / Bridger, R. / Veillon, L. / Azadi, P. / Kornhaber, G. / ...Authors: Meng, L. / Forouhar, F. / Thieker, D. / Gao, Z. / Ramiah, A. / Moniz, H. / Xiang, Y. / Seetharaman, J. / Milaninia, S. / Su, M. / Bridger, R. / Veillon, L. / Azadi, P. / Kornhaber, G. / Wells, L. / Montelione, G.T. / Woods, R.J. / Tong, L. / Moremen, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mps.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mps.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 4mps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/4mps ftp://data.pdbj.org/pub/pdb/validation_reports/mp/4mps | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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
#1: Protein | Mass: 36626.277 Da / Num. of mol.: 2 / Fragment: UNP residues 95-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: BN / Gene: rCG_36561, St6gal1 / Plasmid: pGEn2 mammalian expression vector / Cell line (production host): HEK293 / Production host: Homo sapiens (human) References: UniProt: G3V680, UniProt: P13721*PLUS, beta-galactoside alpha-(2,6)-sialyltransferase #2: Sugar | ChemComp-NAG / #3: 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: 1.97 Å3/Da / Density % sol: 37.47 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8 Details: 0.1M Lithium Bromide, 0.1M Tris, pH 8, 40% (v/w) PEG 1000., micro batch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 29, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.7 Å / Num. all: 44235 / Num. obs: 43837 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.089 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.46 / Num. unique all: 4401 / Rsym value: 0.442 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→46.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 167096.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3879 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→46.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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