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Yorodumi- PDB-4zyh: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zyh | ||||||
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Title | Crystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase C119L variant | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / extremophiles / DNA repair / alkylated DNA-protein alkyltransferase | ||||||
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 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Miggiano, R. / Rossi, F. / Rizzi, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein. Authors: Perugino, G. / Miggiano, R. / Serpe, M. / Vettone, A. / Valenti, A. / Lahiri, S. / Rossi, F. / Rossi, M. / Rizzi, M. / Ciaramella, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zyh.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zyh.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/4zyh ftp://data.pdbj.org/pub/pdb/validation_reports/zy/4zyh | HTTPS FTP |
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-Related structure data
Related structure data | 4zydC 4zyeC 4zygC 1wrjS S: Starting model for refinement C: citing same article (ref.) |
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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: 17070.076 Da / Num. of mol.: 1 / Mutation: C119L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ogt, SSO2487 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.63 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: sodium formate 4 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.89 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.45 Å / Num. obs: 7600 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WRJ Resolution: 2.6→40.576 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.576 Å
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Refine LS restraints |
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LS refinement shell |
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