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Yorodumi- PDB-2iya: The crystal structure of macrolide glycosyltransferases: A bluepr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iya | ||||||
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Title | The crystal structure of macrolide glycosyltransferases: A blueprint for antibiotic engineering | ||||||
Components | OLEANDOMYCIN GLYCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / CARBOHYDRATE / GLYCOSYLATION / GLYCOSYLTRANSFERASE / ENZYME / MACROLIDE | ||||||
Function / homology | Function and homology information antibiotic metabolic process / UDP-glycosyltransferase activity / hexosyltransferase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES ANTIBIOTICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Bolam, D.N. / Roberts, S.M. / Proctor, M.R. / Turkenburg, J.P. / Dodson, E.J. / Martinez-Fleites, C. / Yang, M. / Davis, B.G. / Davies, G.J. / Gilbert, H.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: The Crystal Structure of Two Macrolide Glycosyltransferases Provides a Blueprint for Host Cell Antibiotic Immunity. Authors: Bolam, D.N. / Roberts, S.M. / Proctor, M.R. / Turkenburg, J.P. / Dodson, E.J. / Martinez-Fleites, C. / Yang, M. / Davis, B.G. / Davies, G.J. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iya.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iya.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 2iya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/2iya ftp://data.pdbj.org/pub/pdb/validation_reports/iy/2iya | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45712.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES ANTIBIOTICUS (bacteria) / Description: DSMZ NO.40868 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: Q3HTL7, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #3: Chemical | #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: 2.15 Å3/Da / Density % sol: 42.71 % / Description: NONE |
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Crystal grow | Details: 25-26% PEG2KMME, 0.8M NAFORMATE, 0.1M NAACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97945 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.71 Å / Num. obs: 81807 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.845 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102 / 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: 14.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→74.54 Å
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Refine LS restraints |
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