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Yorodumi- PDB-4v2u: Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v2u | ||||||
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Title | Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis | ||||||
Components | SIALYLTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PASTEURELLA DAGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Pavkov-Keller, T. / Schmoelzer, K. / Czabany, T. / Luley-Goedl, C. / Ribitsch, D. / Schwab, H. / Nidetzky, B. / Gruber, K. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v2u.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2u.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 4v2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2u ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2u | HTTPS FTP |
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-Related structure data
Related structure data | 4v38C 4v39C 4v3bC 4v3cC 2ilvS 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
#1: Protein | Mass: 45662.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PASTEURELLA DAGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: K9UUI6 |
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#2: 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: 2.6 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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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