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Yorodumi- PDB-1mgt: CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mgt | ||||||
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Title | CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1 | ||||||
Components | PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE) | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / DNA REPAIR PROTEIN / SUICIDAL ENZYME / HYPERTHERMOSTABILITY | ||||||
Function / homology | Function and homology information methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / DNA repair / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Hashimoto, H. / Inoue, T. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Kai, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. Authors: Hashimoto, H. / Inoue, T. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Kai, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Archaeal O6-Methylguanine-DNA Methyltransferase Authors: Hashimoto, H. / Nishioka, M. / Inoue, T. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Kai, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mgt.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgt.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mgt_validation.pdf.gz | 418 KB | Display | wwPDB validaton report |
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Full document | 1mgt_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 1mgt_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1mgt_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgt ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19545.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Production host: Escherichia coli (E. coli) References: UniProt: O74023, methylated-DNA-[protein]-cysteine S-methyltransferase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.1 % | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: HANGING DROP VAPOR DIFFUSION, pH 8.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Sep 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 17669 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 16.96 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.16 / % possible all: 76.8 |
Reflection | *PLUS Num. obs: 16314 / Num. measured all: 92828 |
Reflection shell | *PLUS % possible obs: 76.8 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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