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Yorodumi- PDB-8rxg: Crystal structure of alpha-keto C-methyl transferase SgvM bound to SAM -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rxg | ||||||
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Title | Crystal structure of alpha-keto C-methyl transferase SgvM bound to SAM | ||||||
Components | Methyltransferase | ||||||
Keywords | TRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseoviridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.813 Å | ||||||
Authors | Gerhardt, S. / Andexer, J.N. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rxg.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rxg.ent.gz | 168.3 KB | Display | PDB format |
PDBx/mmJSON format | 8rxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rxg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8rxg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8rxg_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 8rxg_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/8rxg ftp://data.pdbj.org/pub/pdb/validation_reports/rx/8rxg | HTTPS FTP |
-Related structure data
Related structure data | 8r4zC 8rprC 8rvcC 8rvsC 8rwmC 8rwwC 8rxfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Streptomyces griseoviridis (bacteria) / Plasmid: pET28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: R9UTR3 |
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-Non-polymers , 5 types, 352 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-COI / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-SAM / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.813→63.0857 Å / Num. obs: 39049 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.059 / Rsym value: 0.203 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.813→1.844 Å / Redundancy: 27.5 % / Rmerge(I) obs: 8.708 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1880 / CC1/2: 0.35 / Rsym value: 8.708 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.813→63.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso mean: 53.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.813→63.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.813→1.83 Å
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Refinement TLS params. | Origin x: -0.4658 Å / Origin y: 23.2931 Å / Origin z: -3.5484 Å
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Refinement TLS group |
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