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Open data
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Basic information
Entry | Database: PDB / ID: 8bir | ||||||
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Title | O-Methyltransferase Plu4895 in complex with SAH and AQ-256 | ||||||
![]() | methyltransferase Plu4895 | ||||||
![]() | 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 | ![]() | 271.1 KB | Display | ![]() |
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PDB format | ![]() | 219.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bgtC ![]() 8bgxC ![]() 8bgyC ![]() 8bgzC ![]() 8bh0C ![]() 8bibC ![]() 8bicC ![]() 8bidC ![]() 8bieC ![]() 8bifC ![]() 8bigSC ![]() 8bihC ![]() 8biiC ![]() 8bijC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38435.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 6 types, 52 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/QOI.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QOI.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-NA / | #7: 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: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammonium iodide, 20% PEG3350 |
-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: Nov 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46 Å / Num. obs: 25372 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2 / Num. unique obs: 2905 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8BIG Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 32.51 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R: 0.875 / ESU R Free: 0.347 / 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: 65.207 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→30 Å
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Refine LS restraints |
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