+Open data
-Basic information
Entry | Database: PDB / ID: 3tsa | ||||||
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Title | Spinosyn Rhamnosyltransferase SpnG | ||||||
Components | NDP-rhamnosyltransferase | ||||||
Keywords | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | Function and homology information cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / enzyme binding Similarity search - Function | ||||||
Biological species | Saccharopolyspora spinosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.7 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 | 3tsa.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tsa.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 3tsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tsa_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 3tsa_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 3tsa_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 3tsa_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/3tsa ftp://data.pdbj.org/pub/pdb/validation_reports/ts/3tsa | HTTPS FTP |
-Related structure data
Related structure data | 3uykC 3uylC 2p6pS 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: 41356.090 Da / Num. of mol.: 2 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 | ChemComp-MG / | #3: Sugar | ChemComp-GLC / | #4: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 18% w/v PEG3350, 1% v/v glycerol, 13% w/v glucose, 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 31, 2010 |
Radiation | Monochromator: micromax / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.41 Å / Num. all: 76134 / Num. obs: 72305 / % possible obs: 89.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 2P6P Resolution: 1.7→19.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.17 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.533 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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