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- PDB-4x7u: MycF mycinamicin III 3'-O-methyltransferase in complex with Mg, S... -
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Open data
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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) | ||||||
![]() | Mycinamicin III 3''-O-methyltransferase![]() | ||||||
![]() | Transferase/Antibiotic / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bernard, S.M. / Smith, J.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 183.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x7vC ![]() 4x7wC ![]() 4x7xC ![]() 4x7yC ![]() 4x7zC ![]() 4x81C ![]() 4xvySC ![]() 4xvzC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q49492, ![]() #2: Chemical | #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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