+Open data
-Basic information
Entry | Database: PDB / ID: 4xvz | ||||||
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Title | MycF mycinamicin III 3'-O-methyltransferase in complex with Mg | ||||||
Components | Mycinamicin III 3''-O-methyltransferase | ||||||
Keywords | TRANSFERASE / macrolide / methyltransferase / antibiotic / natural product | ||||||
Function / homology | Function and homology information mycinamicin III 3''-O-methyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / small molecule binding / methylation / magnesium ion binding Similarity search - Function | ||||||
Biological species | Micromonospora griseorubida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å | ||||||
Authors | Akey, D.L. / Smith, J.L. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O-Methyltransferases. Authors: Bernard, S.M. / Akey, D.L. / Tripathi, A. / Park, S.R. / Konwerski, J.R. / Anzai, Y. / Li, S. / Kato, F. / Sherman, D.H. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xvz.cif.gz | 331.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xvz.ent.gz | 281 KB | Display | PDB format |
PDBx/mmJSON format | 4xvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/4xvz ftp://data.pdbj.org/pub/pdb/validation_reports/xv/4xvz | HTTPS FTP |
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-Related structure data
Related structure data | 4x7uC 4x7vC 4x7wC 4x7xC 4x7yC 4x7zC 4x81C 4xvyC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 32164.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Plasmid: pMCSG7-mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | Temperature: 293.1 K / Method: vapor diffusion / Details: 20-30% PEG 3350, 100 mM BisTrisPropane, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97944 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2010 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→86.85 Å / Num. obs: 36246 / % possible obs: 100 % / Redundancy: 5.8 % / Rsym value: 0.08 / Net I/σ(I): 13.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.49→45.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 16.63 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.239 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.453 Å2
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Refinement step | Cycle: 1 / Resolution: 2.49→86.84 Å
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Refine LS restraints |
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