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Open data
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Basic information
Entry | Database: PDB / ID: 8bgy | ||||||
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Title | O-Methyltransferase Plu4890 in complex with SAH and AQ-284a | ||||||
![]() | Methyltransferase Plu4890 | ||||||
![]() | TRANSFERASE / methyltransferase / polyketide / anthraquinone | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, E.M. / Groll, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / Bode, H.B. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 540.5 KB | Display | ![]() |
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PDB format | ![]() | 448.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 67 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bgtSC ![]() 8bgxC ![]() 8bgzC ![]() 8bh0C ![]() 8bibC ![]() 8bicC ![]() 8bidC ![]() 8bieC ![]() 8bifC ![]() 8bigC ![]() 8bihC ![]() 8biiC ![]() 8bijC ![]() 8birC S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36550.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 449 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/QP3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QP3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-QP3 / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium acetate, 0.1 M Sodium cacodylate pH 6.5, 30 % PEG8000 |
-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: May 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48 Å / Num. obs: 116636 / % possible obs: 97 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2 / Num. unique obs: 15941 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8BGT Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.023 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 78.28 Å2 / Biso mean: 38.747 Å2 / Biso min: 22.39 Å2
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Refinement step | Cycle: final / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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