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Yorodumi- PDB-4zyg: Crystal structure of methylated Sulfolobus solfataricus O6-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zyg | ||||||
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Title | Crystal structure of methylated Sulfolobus solfataricus O6-methylguanine methyltransferase | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / extremophiles / DNA repair / alkylated DNA-protein alkyltransferase / methylated protein | ||||||
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: 2.8 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 | 4zyg.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zyg.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zyg_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 4zyg_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 4zyg_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4zyg_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/4zyg ftp://data.pdbj.org/pub/pdb/validation_reports/zy/4zyg | HTTPS FTP |
-Related structure data
Related structure data | 4zydC 4zyeC 4zyhC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17074.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: ogt, SSO2487 / Plasmid: pQE31 / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: Ammonium acetate 0.1 M, Bis-Tris 0.1 M pH 5.5, 17% PEG 17000 PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.35 Å / Num. obs: 8764 / % possible obs: 97.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.1 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WRJ Resolution: 2.8→47.35 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1 / 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: 2.8→47.35 Å
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Refine LS restraints |
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LS refinement shell |
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