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Yorodumi- PDB-4v3c: The structure of alpha2,3-sialyltransferase variant 2 from Pasteu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v3c | ||||||
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Title | The structure of alpha2,3-sialyltransferase variant 2 from Pasteurella dagmatis in complex with the donor product CMP | ||||||
Components | SIALYLTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PASTEURELLA DAGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 | 4v3c.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3c.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 4v3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v3c_validation.pdf.gz | 807 KB | Display | wwPDB validaton report |
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Full document | 4v3c_full_validation.pdf.gz | 810.1 KB | Display | |
Data in XML | 4v3c_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 4v3c_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3c ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3c | HTTPS FTP |
-Related structure data
Related structure data | 4v2uSC 4v38C 4v39C 4v3bC S: Starting model for refinement C: citing same article (ref.) |
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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: 45642.938 Da / Num. of mol.: 1 / Mutation: YES 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: Chemical | ChemComp-C / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Details: 6.7 MG/ML PROTEIN CONCENTRATION 0.1M SODIUM CITRATE, 20% W/V PEG 3000, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→96 Å / Num. obs: 44015 / % possible obs: 99.5 % / Observed criterion σ(I): 1.8 / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.84→1.92 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V2U Resolution: 1.84→96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.749 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 40.935 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→96 Å
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Refine LS restraints |
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