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Yorodumi- PDB-2bpg: STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bpg | ||||||
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Title | STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA COMPLEX | ||||||
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 / salivary gland morphogenesis ...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 / salivary gland morphogenesis / 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 / spleen development / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / 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 / DNA replication / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / DNA damage response / apoptotic process / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.6 Å | ||||||
Authors | Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J. | ||||||
Citation | 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. / Kumar, A. / Wilson, S.H. / Kraut, J. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bpg.cif.gz | 159 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bpg.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bpg ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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 |
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-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.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P06766 |
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-Non-polymers , 3 types, 7 molecules
#4: Chemical | ChemComp-MG / | ||
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#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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: other | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
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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 | ||||||||||||
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Refinement | Resolution: 3.6→20 Å / σ(F): 0 / σ(I): 0 /
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Refinement step | Cycle: LAST / Resolution: 3.6→20 Å
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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
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