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Yorodumi- PDB-7dqq: Crystal structure of Sulfurisphaera tokodaii O6-methylguanine met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dqq | ||||||
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Title | Crystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant in complex with O6-methyldeoxyguanosine | ||||||
Components | Methylated-DNA--protein-cysteine methyltransferase | ||||||
Keywords | TRANSFERASE / methyltramsferase | ||||||
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: 2.6 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 | 7dqq.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dqq.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dqq_validation.pdf.gz | 672.4 KB | Display | wwPDB validaton report |
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Full document | 7dqq_full_validation.pdf.gz | 672.7 KB | Display | |
Data in XML | 7dqq_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7dqq_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/7dqq ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dqq | HTTPS FTP |
-Related structure data
Related structure data | 7csmC 7d4vC 7dknC 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: 17944.887 Da / Num. of mol.: 1 / Mutation: Y91F, C120S 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 | ChemComp-J03 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 5% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→48.47 Å / Num. obs: 5304 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 32.3 / Num. measured all: 33206 | ||||||||||||||||||||||||||||||
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: 2.6→38.236 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.836 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.179 / SU B: 11.548 / SU ML: 0.247 / Average fsc free: 0.9099 / Average fsc work: 0.9365 / Cross valid method: FREE R-VALUE / ESU R Free: 0.379 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: 27.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→38.236 Å
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Refine LS restraints |
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LS refinement shell |
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