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Yorodumi- PDB-3iaa: Crystal Structure of CalG2, Calicheamicin Glycosyltransferase, TD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iaa | ||||||
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Title | Crystal Structure of CalG2, Calicheamicin Glycosyltransferase, TDP bound form | ||||||
Components | CalG2 | ||||||
Keywords | TRANSFERASE / Glycosyltransferase / Calicheamicin / CalG2 / TDP / enediyne | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Micromonospora echinospora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.505 Å | ||||||
Authors | Chang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity. Authors: Chang, A. / Singh, S. / Helmich, K.E. / Goff, R.D. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iaa.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iaa.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/3iaa ftp://data.pdbj.org/pub/pdb/validation_reports/ia/3iaa | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 45795.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: calG2, Q8KNE0 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNE0 #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 53.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Protein Solution (20 mg/ml CalG4 Protein, 0.05 M NaCl, 0.015 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (0.8M Na3Citrate, 0.1M BisTris pH 6.5) Cryoprotected with 20% ethylene ...Details: Protein Solution (20 mg/ml CalG4 Protein, 0.05 M NaCl, 0.015 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (0.8M Na3Citrate, 0.1M BisTris pH 6.5) Cryoprotected with 20% ethylene glycol, 0.8M Na3Citrate, 0.1M BisTris pH 6.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97957 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2009 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 30322 / % possible obs: 96.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.162 / Χ2: 1.099 / Net I/σ(I): 5.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 54.69
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.505→49.761 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.833 / SU ML: 2.49 / σ(F): 0.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.387 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.51 Å2 / Biso mean: 26.08 Å2 / Biso min: 8.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.505→49.761 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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