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Yorodumi- PDB-7dqt: Crystal structure of O6-methylguanine methyltransferase Y91F variant -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dqt | ||||||
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Title | Crystal structure of O6-methylguanine methyltransferase Y91F variant | ||||||
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: 1.13 Å | ||||||
Authors | Kikuchi, M. / Iizuka, Y. / Yamauchi, T. / 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 | 7dqt.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dqt.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 7dqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dqt_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 7dqt_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 7dqt_validation.xml.gz | 11 KB | Display | |
Data in CIF | 7dqt_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/7dqt ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dqt | HTTPS FTP |
-Related structure data
Related structure data | 7csmC 7d4vC 7dknC 7dqqC 7dqrC 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: 18008.951 Da / Num. of mol.: 1 / Mutation: Y91F 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: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH) |
-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 2M / Detector: PIXEL / Date: Nov 19, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.13→40.17 Å / Num. obs: 59665 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 26.1 / Num. measured all: 755764 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
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: 1.13→30.938 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.429 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.038 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: 11.823 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→30.938 Å
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Refine LS restraints |
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LS refinement shell |
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