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Yorodumi- PDB-8aes: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aes | ||||||
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Title | Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / Self-labelling protein tag / rational mutagenesis / O6-alkylguanine-DNA alkyltransferase / CLIP-tag. | ||||||
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 | Saccharolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Genta, M. / Perugino, G. / Miggiano, R. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2022 Title: First thermostable CLIP- tag by rational design applied to an archaeal O 6 -alkyl-guanine-DNA-alkyl-transferase. Authors: Merlo, R. / Mattossovich, R. / Genta, M. / Valenti, A. / Di Mauro, G. / Minassi, A. / Miggiano, R. / Perugino, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aes.cif.gz | 300.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aes.ent.gz | 245.1 KB | Display | PDB format |
PDBx/mmJSON format | 8aes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aes_validation.pdf.gz | 522.1 KB | Display | wwPDB validaton report |
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Full document | 8aes_full_validation.pdf.gz | 548.5 KB | Display | |
Data in XML | 8aes_validation.xml.gz | 52.7 KB | Display | |
Data in CIF | 8aes_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/8aes ftp://data.pdbj.org/pub/pdb/validation_reports/ae/8aes | HTTPS FTP |
-Related structure data
Related structure data | 4zyeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
-Components
#1: Protein | Mass: 19049.176 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Gene: ogt, SSO2487 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase #2: Water | ChemComp-HOH / | |
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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: 2.85 Å3/Da / Density % sol: 56.82 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M tri-Potassium citrate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 193.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.38 Å / Num. obs: 53272 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 57.23 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Rmerge(I) obs: 0.756 / Num. unique obs: 7791 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4zye Resolution: 2.8→47.38 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.91 / Stereochemistry target values: ML
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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 max: 125.24 Å2 / Biso mean: 54.9617 Å2 / Biso min: 26.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→47.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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