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- PDB-8c9s: Catechol O-methyltransferase from Streptomyces avermitilis in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c9s | ||||||
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Title | Catechol O-methyltransferase from Streptomyces avermitilis in complex with SAH | ||||||
![]() | Putative O-methyltransferase | ||||||
![]() | 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 / pyrrolidin-2-one / S-ADENOSYL-L-HOMOCYSTEINE / Putative O-methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. / Groves, M.R. | ||||||
Funding support | European Union, 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.4 KB | Display | ![]() |
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PDB format | ![]() | 141.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 966.2 KB | Display | ![]() |
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Full document | ![]() | 968 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c9tC ![]() 8c9vC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 25215.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAVERM_5837 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium formate, 10% w/v Polyvinylpyrrolidone 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 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: 1.8→46.09 Å / Num. obs: 36681 / % possible obs: 99.2 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 1.406 / Num. unique obs: 2144 / CC1/2: 0.603 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 22.338 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.09 Å
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Refine LS restraints |
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LS refinement shell |
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