[English] 日本語
![](img/lk-miru.gif)
- PDB-2bpg: STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2bpg | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 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 / 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 / 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 / DNA replication / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
![]() | ![]() Title: Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. #1: ![]() Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 121.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 536.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 621.7 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: ASN B 245 - GLU B 249 OMEGA = 329.09 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATIO | ||||||||
Details | THE FIRST COMPLEX IN THE ASYMMETRIC UNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS A, T, AND P FOR THE PROTEIN MOLECULE, TEMPLATE, AND PRIMER, RESPECTIVELY, AND THE SECOND COMPLEX IN THE ASYMMETRIC UNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS B, C, AND D FOR THE SECOND PROTEIN MOLECULE, TEMPLATE, AND PRIMER, RESPECTIVELY. |
-
Components
-DNA chain , 2 types, 4 molecules TCPD
#1: DNA chain | Mass: 2468.617 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 2099.387 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 38388.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 3 types, 7 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / | ||
---|---|---|---|
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.66 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: other | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ![]() |
---|---|
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 3.6 Å / Num. all: 25046 / Num. obs: 10650 / % possible obs: 96 % |
Reflection | *PLUS Highest resolution: 3.6 Å / % possible obs: 96 % |
-
Processing
Software | Name: TNT / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.6→20 Å / σ(F): 0 / σ(I): 0 /
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→20 Å
| ||||||||||||
Refinement | *PLUS Highest resolution: 3.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.199 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|