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Yorodumi- PDB-1bpd: CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMM... -
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-Basic information
Entry | Database: PDB / ID: 1bpd | ||||||
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Title | CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM | ||||||
Components | DNA POLYMERASE BETA | ||||||
Keywords | NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / 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 / in utero embryonic development / microtubule / DNA replication / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.6 Å | ||||||
Authors | Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
Citation | Journal: Science / Year: 1994 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. #1: Journal: Science / Year: 1994 Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template-Primer, and ddCTP Authors: Pelletier, H. / Sawaya, M.R. / Wilson, S.H. / Kraut, J. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Studies of the Domain Structure of Mammalian DNA Polymerase Beta. Identification of a Discrete Template Binding Domain Authors: Kumar, A. / Widen, S.G. / Williams, K.R. / Kedar, P. / Karpel, R.L. / Wilson, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bpd.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bpd.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bpd ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bpd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38388.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P06766, DNA-directed DNA polymerase | ||
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#2: Chemical | ChemComp-PO4 / | ||
Nonpolymer details | RESIDUE PHO IS PROBABLY PHOSPHATE OR SULFATE ANION IN THE DEOXYNUCLESequence details | THE N-TERMINAL METHIONINE IS INCLUDED IN THE GENE SEQUENCE EVEN THOUGH IT IS REMOVED AFTER ...THE N-TERMINAL METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3.6 Å / Num. obs: 4153 / Num. measured all: 14621 / Rmerge(I) obs: 0.072 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.6→20 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 3.6→20 Å
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Refine LS restraints |
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