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- PDB-3rb3: Dpo4 extension ternary complex with 3'-terminal primer A base opp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rb3 | ||||||
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Title | Dpo4 extension ternary complex with 3'-terminal primer A base opposite the 1-methylguanine (m1g) lesion | ||||||
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![]() | 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 / 1-methylguanine | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rechkoblit, O. / Patel, D.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.3 KB | Display | ![]() |
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PDB format | ![]() | 149.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3raqSC ![]() 3raxC ![]() 3rb0C ![]() 3rb4C ![]() 3rb6C ![]() 3rbdC ![]() 3rbeC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38945.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules DE
#2: DNA chain | Mass: 4070.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic |
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#3: DNA chain | Mass: 5981.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic |
-Non-polymers , 4 types, 40 molecules ![](data/chem/img/DGT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DGT / | ||||
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#5: Chemical | #6: Chemical | ChemComp-EPE / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.81 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2005 |
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: 2.8→20 Å / Num. obs: 13492 / % possible obs: 94.4 % / Observed criterion σ(F): 3.6 / Observed criterion σ(I): 3.6 / Redundancy: 4.6 % |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 3.3 % / % possible all: 83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RAQ Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / SU B: 39.115 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 3.5 / ESU R Free: 0.403 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.386 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 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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