[English] 日本語
Yorodumi- PDB-5llq: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5llq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase C119F variant | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / DNA dealkylation / OGT / inactive mutant | ||||||
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: 2.7 Å | ||||||
Authors | Miggiano, R. / Rossi, F. / Rizzi, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5llq.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5llq.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 5llq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5llq ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5llq | HTTPS FTP |
---|
-Related structure data
Related structure data | 4zyeS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Gene: ogt, SSO2487 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.19 % / Description: Thin needle |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.24 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|