+Open data
-Basic information
Entry | Database: PDB / ID: 8fts | ||||||
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Title | SgvM methyltransferase with SAH and alpha-ketoleucine | ||||||
Components | Methyltransferase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseoviridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kuzelka, K. / Nair, S.K. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: A biocatalytic platform for asymmetric alkylation of alpha-keto acids by mining and engineering of methyltransferases Authors: Ju, S. / Kuzelka, K.P. / Guo, R. / Krohn-Hansen, B. / Wu, J. / Nair, S.K. / Yang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fts.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fts.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/8fts ftp://data.pdbj.org/pub/pdb/validation_reports/ft/8fts | HTTPS FTP |
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-Related structure data
Related structure data | 8ftrC 8ftvC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36911.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R9UTR3 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-COI / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / Details: PEG 3350 pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38.133 Å / Num. obs: 23134 / % possible obs: 99.4 % / Redundancy: 21.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.2→2.207 Å / Rmerge(I) obs: 1.823 / Num. unique obs: 5110 / CC1/2: 0.792 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.65 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.487 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→25 Å
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Refine LS restraints |
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