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- PDB-4m71: Mutant structure of methyltransferase from Streptomyces hygroscop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m71 | |||||||||
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Title | Mutant structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic acid | |||||||||
![]() | Methyltransferase MppJ | |||||||||
![]() | TRANSFERASE / Rossmann Fold / Methyltransferase / SAM/PPY Binding | |||||||||
Function / homology | ![]() phenylpyruvate C3-methyltransferase / antibiotic biosynthetic process / methyltransferase activity / methylation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, Y.C. / Zou, X.W. / Chan, H.C. / Huang, C.J. / Li, T.L. | |||||||||
![]() | ![]() Title: Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase Authors: Zou, X.W. / Liu, Y.C. / Hsu, N.S. / Huang, C.J. / Lyu, S.Y. / Chan, H.C. / Chang, C.Y. / Yeh, H.W. / Lin, K.H. / Wu, C.J. / Tsai, M.D. / Li, T.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 | ![]() | 160.4 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1013.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kibSC ![]() 4kicC ![]() 4kifC ![]() 4kigC ![]() 4m6xC ![]() 4m6yC ![]() 4m72C ![]() 4m73C ![]() 4m74C S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37198.922 Da / Num. of mol.: 2 / Mutation: R127L, D244E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q643C8, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 7 types, 552 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/56D.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HF2.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/56D.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HF2.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-IOD / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG3350, 0.2M sodium iodine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 19, 2013 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 34611 / Num. obs: 34611 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KIB Resolution: 2.21→28.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.391 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.264 / ESU R Free: 0.218 / 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: 31.392 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.263 Å / Total num. of bins used: 20
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