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Yorodumi- PDB-3rbd: Dpo4 extension ternary complex with 3'-terminal primer C base opp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rbd | ||||||
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Title | Dpo4 extension ternary complex with 3'-terminal primer C base opposite the 3-methylcytosine (m3c) lesion | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA DAMAGE / DNA REPAIR / DNA REPLICATION / DNA-BINDING / DNA-DIRECTED DNA POLYMERASE / MAGNESIUM / METAL-BINDING / MUTATOR PROTEIN / NUCLEOTIDYLTRANSFERASE / TRANSFERASE / TRANSFERASE-DNA COMPLEX / Lesion bypass / DNA polymerase / Y-family polymerase / dNTP-binding / 3-methylcytosine | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Rechkoblit, O. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Authors: Rechkoblit, O. / Delaney, J.C. / Essigmann, J.M. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rbd.cif.gz | 357.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rbd.ent.gz | 286.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/3rbd ftp://data.pdbj.org/pub/pdb/validation_reports/rb/3rbd | HTTPS FTP |
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-Related structure data
Related structure data | 3raqC 3raxC 3rb0C 3rb3C 3rb4SC 3rb6C 3rbeC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38945.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL Codon plus / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 4 molecules DHEJ
#2: DNA chain | Mass: 4046.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic #3: DNA chain | Mass: 5942.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic |
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-Non-polymers , 4 types, 129 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-EPE / | #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: 2.92 Å3/Da / Density % sol: 57.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, pH 7.0, 100 mM calcium acetate and 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2006 |
Radiation | Monochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 37440 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.5→2.5 Å / Redundancy: 2.9 % / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RB4 Resolution: 2.502→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 19.868 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.669 Å2
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Refinement step | Cycle: LAST / Resolution: 2.502→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.566 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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