+Open data
-Basic information
Entry | Database: PDB / ID: 8c9t | ||||||
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Title | Catechol O-methyltransferase from Streptomyces avermitilis | ||||||
Components | Putative O-methyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / O-methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Putative O-methyltransferase Function and homology information | ||||||
Biological species | Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Zhang, L. / Groves, M.R. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: Structural Characterization and Extended Substrate Scope Analysis of Two Mg 2+ -Dependent O-Methyltransferases from Bacteria. Authors: Sokolova, N. / Zhang, L. / Deravi, S. / Oerlemans, R. / Groves, M.R. / Haslinger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c9t.cif.gz | 351.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c9t.ent.gz | 279 KB | Display | PDB format |
PDBx/mmJSON format | 8c9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/8c9t ftp://data.pdbj.org/pub/pdb/validation_reports/c9/8c9t | HTTPS FTP |
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-Related structure data
Related structure data | 8c9sC 8c9vC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25215.326 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria) Gene: SAVERM_5837 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82B68 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M MIB(Malonic acid,Imidazole,Boric acid) pH6.0; 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.71 Å / Num. obs: 131969 / % possible obs: 96.2 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.278 / Num. unique obs: 5286 / CC1/2: 0.967 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.093 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.074 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.71 Å
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Refine LS restraints |
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LS refinement shell |
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