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Yorodumi- PDB-1t38: HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAININ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t38 | ||||||
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Title | HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE | ||||||
Components |
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Keywords | TRANSFERASE/DNA / ALKYLTRANSFERASE / METHYLTRANSFERASE / DNA REPAIR / HELIX-TURN-HELIX / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA ligation / DNA alkylation repair / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair ...MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA ligation / DNA alkylation repair / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair / negative regulation of apoptotic process / DNA binding / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Daniels, D.S. / Woo, T.T. / Luu, K.X. / Noll, D.M. / Clarke, N.D. / Pegg, A.E. / Tainer, J.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: DNA binding and nucleotide flipping by the human DNA repair protein AGT. Authors: Daniels, D.S. / Woo, T.T. / Luu, K.X. / Noll, D.M. / Clarke, N.D. / Pegg, A.E. / Tainer, J.A. #1: Journal: Embo J. / Year: 2000 Title: Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding Authors: Daniels, D.S. / Mol, C.D. / Arvai, A.S. / Kanugula, S. / Pegg, A.E. / Tainer, J.A. #2: Journal: Mutat.Res. / Year: 2000 Title: Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase Authors: Daniels, D.S. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t38.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t38.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 1t38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t38 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t38 | HTTPS FTP |
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-Related structure data
Related structure data | 1t39C 1eh6S 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: DNA chain | Mass: 4005.637 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 20339.408 Da / Num. of mol.: 1 / Mutation: C145S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.1 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3000, Tris, sodium chloride, xylitol, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→46 Å / Num. obs: 6205 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EH6 Resolution: 3.2→29.32 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 4747888.28 / Data cutoff high rms absF: 4747888.28 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5433 Å2 / ksol: 0.206121 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→29.32 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.2 Å / Total num. of bins used: 6 /
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Xplor file |
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