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- PDB-3rh6: DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated prime... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rh6 | ||||||
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Title | DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) | ||||||
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![]() | TRANSFERASE/DNA / polymerase beta / ribonucleotide insertion / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / microtubule / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cavanaugh, N.A. / Beard, W.A. / Batra, V.K. / Perera, L. / Pedersen, L.G. / Wilson, S.H. | ||||||
![]() | ![]() Title: Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. Authors: Cavanaugh, N.A. / Beard, W.A. / Batra, V.K. / Perera, L. / Pedersen, L.G. / Wilson, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112 KB | Display | ![]() |
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PDB format | ![]() | 79.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rh4C ![]() 3rh5C ![]() 2fmsS C: citing same article ( S: Starting model for refinement |
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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: 38149.578 Da / Num. of mol.: 1 / Mutation: Y271A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-DNA chain , 3 types, 3 molecules TPD
#2: DNA chain | Mass: 4829.133 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | ( Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: DNA chain | ( Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 336 molecules ![](data/chem/img/CTP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MN / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 16% PEG3350, 350 mM sodium acetate, 50 mM imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 24, 2009 / Details: Viramax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.048→20.77 Å / Num. all: 25790 / Num. obs: 25790 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FMS Resolution: 2.048→20.77 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 28.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.573 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.048→20.77 Å
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Refine LS restraints |
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LS refinement shell |
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