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Yorodumi- PDB-3uyl: Spinosyn Rhamnosyltransferase SpnG complexed with thymidine dipho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uyl | ||||||
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Title | Spinosyn Rhamnosyltransferase SpnG complexed with thymidine diphosphate | ||||||
Components | NDP-rhamnosyltransferase | ||||||
Keywords | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Saccharopolyspora spinosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Isiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structural Studies of the Spinosyn Rhamnosyltransferase, SpnG. Authors: Isiorho, E.A. / Liu, H.W. / Keatinge-Clay, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uyl.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uyl.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 3uyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uyl ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uyl | HTTPS FTP |
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-Related structure data
Related structure data | 3tsaSC 3uykC 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: 40943.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnG / Production host: Escherichia coli (E. coli) References: UniProt: Q9ALM8, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-GLC / | #5: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT RESIDUE ALA 360 IS CORRECT. | |
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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: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 18% w/v PEG3350, 12.5-13.5% w/v glucose, 1% v/v glycerol, 0.1 M magnesium formate, 0.1 M sodium cacodylate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010 |
Radiation | Monochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→24.62 Å / Num. all: 66093 / Num. obs: 57920 / % possible obs: 92.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.85→1.9 Å / % possible all: 88.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TSA Resolution: 1.85→24.62 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.84 / SU B: 5.337 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.182 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→24.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.855→1.903 Å / Total num. of bins used: 20
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