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- PDB-4v2u: Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis -
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Open data
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Basic information
Entry | Database: PDB / ID: 4v2u | ||||||
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Title | Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis | ||||||
![]() | SIALYLTRANSFERASE | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pavkov-Keller, T. / Schmoelzer, K. / Czabany, T. / Luley-Goedl, C. / Ribitsch, D. / Schwab, H. / Nidetzky, B. / Gruber, K. | ||||||
![]() | ![]() Title: Complete Switch from Alpha2,3- to Alpha2,6-Regioselectivity in Pasteurella Dagmatis Beta-D-Galactoside Sialyltransferase by Active-Site Redesign Authors: Schmoelzer, K. / Czabany, T. / Pavkov-Keller, T. / Luley-Goedl, C. / Ribitsch, D. / Schwab, H. / Gruber, K. / Nidetzky, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.1 KB | Display | ![]() |
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PDB format | ![]() | 69.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
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Full document | ![]() | 428.9 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v38C ![]() 4v39C ![]() 4v3bC ![]() 4v3cC ![]() 2ilvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45662.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | Details: 3.3 MG/ML OF PROTEIN INDEX SCREEN CONDITION D9 (0.1M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PILATUS / Detector: PIXEL / Date: Jan 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→45.1 Å / Num. obs: 12618 / % possible obs: 98.8 % / Observed criterion σ(I): 1.9 / Redundancy: 3.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.71→2.87 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ILV Resolution: 2.71→45.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.81 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY RESIDUES 36-39 ARE DISORDERED OR SHOW MULTIPLE CONFORMATIONS AND COULD NOT BE BUILD WITH CERTAINTY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.174 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→45.11 Å
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Refine LS restraints |
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