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Yorodumi- PDB-7dqr: Crystal structure of Sulfurisphaera tokodaii methylated O6-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dqr | ||||||
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Title | Crystal structure of Sulfurisphaera tokodaii methylated 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: 1.74 Å | ||||||
Authors | Kikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsonoda, 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. / Tsonoda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dqr.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dqr.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 7dqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dqr_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 7dqr_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 7dqr_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 7dqr_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/7dqr ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dqr | HTTPS FTP |
-Related structure data
Related structure data | 7csmC 7d4vC 7dknC 7dqqC 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: 17990.979 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 | ChemComp-SO4 / |
#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: 2.16 Å3/Da / Density % sol: 43.03 % |
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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: 1.74→48.21 Å / Num. obs: 16659 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Net I/σ(I): 34.8 / Num. measured all: 107753 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wrj Resolution: 1.74→39.992 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.196 / SU B: 2.022 / SU ML: 0.068 / Average fsc free: 0.9358 / Average fsc work: 0.9488 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.116 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: 22.152 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→39.992 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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