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Yorodumi- PDB-3m9n: Crystal Structure of Dpo4 in complex with DNA containing the majo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m9n | ||||||
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Title | Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion | ||||||
Components |
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Keywords | Transferase/DNA / Dpo4 / translesion DNA synthesis / TLS / cisplatin / Y-family DNA polymerase / protein-DNA complex / DNA / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / Transferase-DNA complex | ||||||
Function / homology | Function and homology information error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Wong, J.H.Y. / Ling, H. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4. Authors: Wong, J.H. / Brown, J.A. / Suo, Z. / Blum, P. / Nohmi, T. / Ling, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m9n.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m9n.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 3m9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9n ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9n | HTTPS FTP |
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-Related structure data
Related structure data | 3m9mC 3m9oC 1jx4S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 40257.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 4114.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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#3: DNA chain | Mass: 5345.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
-Non-polymers , 4 types, 297 molecules
#4: Chemical | #5: Chemical | ChemComp-CTP / | #6: Chemical | ChemComp-CPT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: 0.2M calcium acetate, 5% glycerol, 15% PEG 3350, 200mM NaCl, pH 7.5, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC Q315 / Detector: CCD / Date: Nov 28, 2007 |
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 40879 / Num. obs: 40552 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.474 / Num. unique all: 1838 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JX4 Resolution: 1.93→27.6 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.815 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 41.101 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.42 Å2 / Biso mean: 33.821 Å2 / Biso min: 14.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→27.6 Å
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Refine LS restraints |
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Xplor file |
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