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Yorodumi- PDB-4v39: Apo-structure of alpha2,3-sialyltransferase variant 2 from Pasteu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v39 | ||||||
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Title | Apo-structure of alpha2,3-sialyltransferase variant 2 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: 2.6 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 | 4v39.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v39.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 4v39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v39_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 4v39_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 4v39_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4v39_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v39 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v39 | HTTPS FTP |
-Related structure data
Related structure data | 4v2uSC 4v38C 4v3bC 4v3cC 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: 6.7 MG/ML PROTEIN CONCENTRATION 0.1M CITRATE, 20%W/V PEG 6000, PH 5.0 |
-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: 2.34→52.3 Å / Num. obs: 22648 / % possible obs: 99.2 % / Observed criterion σ(I): 2.1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.34→2.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V2U Resolution: 2.6→74.21 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.584 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 1.247 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REGION AA35-40 IS FLEXIBLE 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: 36.837 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→74.21 Å
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Refine LS restraints |
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