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Yorodumi- PDB-2wnf: Crystal Structure of a Mammalian Sialyltransferase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wnf | |||||||||
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Title | Crystal Structure of a Mammalian Sialyltransferase in complex with Gal-beta-1-3GalNAc-ortho-nitrophenol | |||||||||
Components | CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE | |||||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / DISULFIDE BOND / GOLGI APPARATUS / SIALYLTRANSFERASE / GLYCOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE / MEMBRANE / SECRETED / SIALIC ACID | |||||||||
Function / homology | Function and homology information beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3-sialyltransferase / beta-galactoside alpha-2,3-sialyltransferase / beta-galactoside (CMP) alpha-2,3-sialyltransferase activity / ganglioside biosynthetic process via lactosylceramide / beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3- sialyltransferase / Golgi medial cisterna membrane / Golgi trans cisterna membrane / N-acetylneuraminate metabolic process / sialylation / protein N-linked glycosylation ...beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3-sialyltransferase / beta-galactoside alpha-2,3-sialyltransferase / beta-galactoside (CMP) alpha-2,3-sialyltransferase activity / ganglioside biosynthetic process via lactosylceramide / beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3- sialyltransferase / Golgi medial cisterna membrane / Golgi trans cisterna membrane / N-acetylneuraminate metabolic process / sialylation / protein N-linked glycosylation / protein glycosylation / trans-Golgi network membrane / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | SUS SCROFA (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Rao, F.V. / Rich, J.R. / Raikic, B. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structural Insight Into Mammalian Sialyltransferases. Authors: Rao, F.V. / Rich, J.R. / Rakic, B. / Buddai, S. / Schwartz, M.F. / Johnson, K. / Bowe, C. / Wakarchuk, W.W. / Defrees, S. / Withers, S.G. / Strynadka, N.C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wnf.cif.gz | 82.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wnf.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wnf ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wnf | HTTPS FTP |
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-Related structure data
Related structure data | 2wmlSC 2wnbC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34747.945 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-343 COMPND 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Plasmid: PCWIN2-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI2 / References: UniProt: Q02745, EC: 2.4.99.4 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen / Thomsen–Friedenreich antigen |
#3: Chemical | ChemComp-CG3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000 AND 0.1 M MES, PH 6.8 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→33.11 Å / Num. obs: 85229 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WML Resolution: 1.25→33.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.324 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→33.11 Å
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Refine LS restraints |
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