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Yorodumi- PDB-7dkn: Crystal structure of Sulfurisphaera tokodaii O6-methylguanine met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dkn | ||||||
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Title | Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
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 | Sulfurisphaera tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Kikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsunoda, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Authors: Kikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsunoda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dkn.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dkn.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dkn_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 7dkn_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 7dkn_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7dkn_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkn ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkn | HTTPS FTP |
-Related structure data
Related structure data | 7csmC 7d4vC 7dqqC 7dqrC 7dqtC 7e1pC 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: 17976.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ogt, STK_09670 / Production host: Escherichia coli (E. coli) References: UniProt: Q973C7, methylated-DNA-[protein]-cysteine S-methyltransferase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→40.052 Å / Num. obs: 15203 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Net I/σ(I): 20.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wrj Resolution: 1.79→40.052 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.514 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.123 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→40.052 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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