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Yorodumi- PDB-6ga0: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ga0 | |||||||||
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Title | Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with SNAP-Vista Green | |||||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | |||||||||
Keywords | TRANSFERASE / O6-alkylguanine-DNA alkyltransferase / protein engineering / self-labeling protein tag / fluorescent probe / extremophiles | |||||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / cytoplasm Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus P2 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Miggiano, R. / Rossi, F. / Rizzi, M. | |||||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with a fluorescent probe. Authors: Rossi, F. / Morrone, C. / Massarotti, A. / Ferraris, D.M. / Valenti, A. / Perugino, G. / Miggiano, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ga0.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ga0.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ga0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ga0_validation.pdf.gz | 713.1 KB | Display | wwPDB validaton report |
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Full document | 6ga0_full_validation.pdf.gz | 715.5 KB | Display | |
Data in XML | 6ga0_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 6ga0_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/6ga0 ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6ga0 | HTTPS FTP |
-Related structure data
Related structure data | 4zyeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19242.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The electron density map is not visible for the N-terminal His-tag and for five residues mapping at the C-terminal, that has been introduced in sub-cloning experiment. Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Gene: ogt, SSO2487 / Production host: Escherichia coli (E. coli) References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase | ||
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#2: Chemical | ChemComp-ETW / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→79.52 Å / Num. obs: 13435 / % possible obs: 98.3 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 1296 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZYE Resolution: 2→79.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.607 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.439 Å2
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Refinement step | Cycle: 1 / Resolution: 2→79.52 Å
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Refine LS restraints |
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