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- PDB-5llq: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5llq | ||||||
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Title | Crystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase C119F variant | ||||||
![]() | Methylated-DNA--protein-cysteine methyltransferase | ||||||
![]() | TRANSFERASE / DNA dealkylation / OGT / inactive mutant | ||||||
Function / homology | ![]() methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miggiano, R. / Rossi, F. / Rizzi, M. | ||||||
![]() | ![]() Title: Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase. Authors: Morrone, C. / Miggiano, R. / Serpe, M. / Massarotti, A. / Valenti, A. / Del Monaco, G. / Rossi, M. / Rossi, F. / Rizzi, M. / Perugino, G. / Ciaramella, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.2 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zyeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18678.805 Da / Num. of mol.: 2 Mutation: Catalytic Cysteine 119 is substituted by Phenilalanine Source method: isolated from a genetically manipulated source Details: Residues belonging to His-tag were not visible in the electron density. For this reason they were removed from coordinates file. Source: (gene. exp.) ![]() ![]() Gene: ogt, SSO2487 / Production host: ![]() ![]() References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % / Description: Thin needle |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0,2 M ammonium phosphate monobasic 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.24 Å / Num. obs: 12411 / % possible obs: 96.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.26 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.35 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZYE Resolution: 2.7→49.24 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.24 Å
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Refine LS restraints |
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LS refinement shell |
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