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Yorodumi- PDB-8rpr: Crystal Structure of SgvM methyltransferase in complex with alpha... -
+Open data
-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 | |||||||||
Components | Methyltransferase | |||||||||
Keywords | TRANSFERASE / complex / Methylransferase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Streptomyces griseoviridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | |||||||||
Authors | Saleem-Batcha, R. / Zou, Z. / Breiltgens, J. / Mueller, M. / Andexer, J.N. | |||||||||
Funding support | Germany, European Union, 2items
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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 | 8rpr.cif.gz | 176 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rpr.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rpr_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8rpr_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8rpr_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8rpr_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/8rpr ftp://data.pdbj.org/pub/pdb/validation_reports/rp/8rpr | HTTPS FTP |
-Related structure data
Related structure data | 8r4zC 8rvcC 8rvsC 8rwmC 8rwwC 8rxfC 8rxgC 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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9UTR3 |
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-Non-polymers , 5 types, 117 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2802 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→47.4 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0603 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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