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- PDB-5u2s: Pre-catalytic ternary complex of Human DNA Polymerase Beta With G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u2s | |||||||||
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Title | Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+. | |||||||||
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![]() | TRANSFERASE/DNA / X-FAMILY / POL BETA / DNA POLYMERASE BETA / 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 | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vyas, R. / Suo, Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the D-stereoselectivity of human DNA polymerase beta. Authors: Vyas, R. / Reed, A.J. / Raper, A.T. / Zahurancik, W.J. / Wallenmeyer, P.C. / Suo, Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 75.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.7 KB | Display | ![]() |
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Full document | ![]() | 733.1 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u2rC ![]() 5u2tC ![]() 4rq7S 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39258.785 Da / Num. of mol.: 1 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 DPT
#2: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 106 molecules ![](data/chem/img/1RZ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-1RZ / | ||||
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#6: Chemical | ChemComp-CA / | ||||
#7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-ACT / #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 MM IMIDAZOLE, 350 MM SODIUM ACETATE, 17% PEG3350 PH range: 8 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.03 Å / Num. obs: 23005 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RQ7 Resolution: 2.3→44.03 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.875 / SU B: 11.856 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.28 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.03 Å
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Refine LS restraints |
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