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Yorodumi- PDB-4zye: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zye | ||||||
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Title | Crystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase | ||||||
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: 1.85 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 | 4zye.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zye.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 4zye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zye_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 4zye_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 4zye_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4zye_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/4zye ftp://data.pdbj.org/pub/pdb/validation_reports/zy/4zye | HTTPS FTP |
-Related structure data
Related structure data | 4zydC 4zygC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18634.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Proline residue before start methionine was inserted in sub-cloning experiment. Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (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 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: potassium nitrate 0.35 M, Ammonium sulfate 1.6 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.364 Å / Num. obs: 21897 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WRJ Resolution: 1.85→47.364 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.5 / 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: 1.85→47.364 Å
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Refine LS restraints |
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LS refinement shell |
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