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Yorodumi- PDB-4x7u: MycF mycinamicin III 3'-O-methyltransferase in complex with Mg, S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x7u | ||||||
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Title | MycF mycinamicin III 3'-O-methyltransferase in complex with Mg, SAH and mycinamicin III (substrate) | ||||||
Components | Mycinamicin III 3''-O-methyltransferase | ||||||
Keywords | Transferase/Antibiotic / macrolide / methyltransferase / antibiotic / natural product / Transferase-Antibiotic complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bernard, S.M. / 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 | 4x7u.cif.gz | 230.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x7u.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 4x7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x7u_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4x7u_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4x7u_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 4x7u_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7u ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7u | HTTPS FTP |
-Related structure data
Related structure data | 4x7vC 4x7wC 4x7xC 4x7yC 4x7zC 4x81C 4xvySC 4xvzC C: citing same article (ref.) S: Starting model for refinement |
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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: 30816.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20-30% PEG 5000 MME, 100 mM ammonium acetate, and 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-B / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 71066 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rsym value: 0.073 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.588 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XVY Resolution: 1.65→43.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.244 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076 / 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: 18.255 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→43.71 Å
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Refine LS restraints |
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