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Yorodumi- PDB-3wag: Crystal structure of glycosyltransferase VinC in complex with DTDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wag | ||||||
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Title | Crystal structure of glycosyltransferase VinC in complex with DTDP | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / VICENISAMINYLTRANSFERASE / VICENISTATIN BIOSYNTHESIS / ANTIBIOTIC | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces halstedii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nango, E. / Minami, A. / Kumasaka, T. / Eguchi, T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Glycosyltransferase VinC Involved in the Biosynthesis of Vicenistatin Authors: Nango, E. / Minami, A. / Kumasaka, T. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wag.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wag.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wag_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3wag_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3wag_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 3wag_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wag ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wag | HTTPS FTP |
-Related structure data
Related structure data | 3wadS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46112.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinC / Production host: Escherichia coli (E. coli) / References: UniProt: Q76KZ6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20 %(W/V) PEG 3350, 0.2M MGCL2, 100MM TRIS, 10MM DTDP, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 29, 2007 |
Radiation | Monochromator: SI 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 52575 / Num. obs: 48895 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WAD Resolution: 2.1→31.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.039 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→31.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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