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- PDB-3uyk: Spinosyn Rhamnosyltransferase SpnG complexed with spinosyn aglycone -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uyk | ||||||
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Title | Spinosyn Rhamnosyltransferase SpnG complexed with spinosyn aglycone | ||||||
![]() | NDP-rhamnosyltransferase | ||||||
![]() | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | ![]() cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.9 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.8 KB | Display | ![]() |
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Full document | ![]() | 813.1 KB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tsaSC ![]() 3uylC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q9ALM8, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-0CX / ( | #4: Sugar | ChemComp-BGC / | #5: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT RESIDUE ALA 360 IS CORRECT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
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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: ![]() ![]() ![]() |
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: 1.7→29.83 Å / Num. all: 84558 / Num. obs: 78024 / % possible obs: 96.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.75 Å / % possible all: 91.99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3TSA Resolution: 1.7→29.83 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.175 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 21.326 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å / Total num. of bins used: 20
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