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- PDB-8rpr: Crystal Structure of SgvM methyltransferase in complex with alpha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rpr | |||||||||
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Title | Crystal Structure of SgvM methyltransferase in complex with alpha-ketoleucine and Zn2+ ion | |||||||||
![]() | Methyltransferase | |||||||||
![]() | TRANSFERASE / complex / Methylransferase | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saleem-Batcha, R. / Zou, Z. / Breiltgens, J. / Mueller, M. / Andexer, J.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures and Protein Engineering of the alpha-Keto Acid C-Methyltransferases SgvM and MrsA for Rational Substrate Transfer. Authors: Sommer-Kamann, C. / Breiltgens, J. / Zou, Z. / Gerhardt, S. / Saleem-Batcha, R. / Kemper, F. / Einsle, O. / Andexer, J.N. / Muller, 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 | ![]() | 176 KB | Display | ![]() |
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PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r4zC ![]() 8rvcC ![]() 8rvsC ![]() 8rwmC ![]() 8rwwC ![]() 8rxfC ![]() 8rxgC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36911.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 117 molecules ![](data/chem/img/COI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-COI / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris/HCl pH 8.5, 250 mM Li2SO4, and 23% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2802 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→47.4 Å / Num. obs: 43575 / % possible obs: 99.1 % / Redundancy: 24.2 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.14→2.25 Å / Rmerge(I) obs: 1.38 / Num. unique obs: 23727 / CC1/2: 0.81 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→47.4 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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