+Open data
-Basic information
Entry | Database: PDB / ID: 2wml | ||||||
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Title | Crystal Structure of a Mammalian Sialyltransferase | ||||||
Components | CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE -ALPHA-2\,3-SIALYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / SIALYLTRANSFERASE / 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 / MAD / Resolution: 1.9 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 | 2wml.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wml.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 2wml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wml ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wml | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34748.996 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-343 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: Chemical | #3: Chemical | ChemComp-CL / | #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: 1.86 Å3/Da / Density % sol: 34 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000, 0.1M MES, PH 6.8 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97965 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2008 / Details: KOHZU DOUBLE CRYSTAL SI(111) |
Radiation | Monochromator: KHOZU DOUBLE FLAT CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97965 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61 Å / Num. obs: 26352 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.8→2.01 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.9→61.16 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.452 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.142 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 46-58 AND 306-314 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→61.16 Å
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Refine LS restraints |
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