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- PDB-8rvc: Crystal structure of alpha keto acid C-methyl-transferases MrsA b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rvc | ||||||
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Title | Crystal structure of alpha keto acid C-methyl-transferases MrsA bound to ketoarginine | ||||||
![]() | 2-ketoarginine methyltransferase | ||||||
![]() | TRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation / asymmetric methylation / mutagenesis | ||||||
Function / homology | ![]() 5-guanidino-2-oxopentanoate (3R)-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gerhardt, S. / Kemper, F. / Andexer, J.N. | ||||||
Funding support | 1items
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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 | ![]() | 402.1 KB | Display | ![]() |
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PDB format | ![]() | 336.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r4zC ![]() 8rvsC ![]() 8rwmC ![]() 8rwwC ![]() 8rxfC 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, 2 molecules AB
#1: Protein | Mass: 40944.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D5FKJ3, 5-guanidino-2-oxopentanoate (3R)-methyltransferase |
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-Non-polymers , 7 types, 389 molecules ![](data/chem/img/NWG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Chemical | ChemComp-NA / #8: 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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES, 300mM potassium chloride, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→49.51 Å / Num. obs: 51937 / % possible obs: 98 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.154 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2612 / CC1/2: 0.755 / Rpim(I) all: 0.318 / Rrim(I) all: 1.033 / % possible all: 71.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 31.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.969→49.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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