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Yorodumi- PDB-1dk2: REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYME... -
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-Basic information
Entry | Database: PDB / ID: 1dk2 | ||||||
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Title | REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA | ||||||
Components | DNA POLYMERASE BETA | ||||||
Keywords | TRANSFERASE / DNA-BINDING / DEOXYRIBOSE 5'-PHOSPHATE LYASE / 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 / 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 / in utero embryonic development / 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 | SOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING | ||||||
Authors | Maciejewski, M.W. / Prasad, R. / Liu, D.-J. / Wilson, S.H. / Mullen, G.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity. Authors: Maciejewski, M.W. / Liu, D. / Prasad, R. / Wilson, S.H. / Mullen, G.P. #1: Journal: Biochemistry / Year: 1996 Title: Three-Dimensional Solution Structure of the N-terminal Domain of DNA Polymerase beta and Mapping of the ssDNA Interaction Interface Authors: Liu, D.-J. / Prasad, R. / Wilson, S.H. / DeRose, E.F. / Mullen, G.P. #2: Journal: Biochemistry / Year: 1994 Title: Assignments of 1H, 15N, and 13C Resonances for the Backbone and Side Chains of the N-terminal Domain of DNA Polymerase beta. Determination of the Secondary Structure and Tertiary Contacts Authors: Liu, D.-J. / DeRose, E.F. / Prasad, R. / Wilson, S.H. / Mullen, G.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dk2.cif.gz | 663 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dk2.ent.gz | 558.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dk2 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dk2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9501.103 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-87 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PRSET-8K / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL EXPRESSION SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131). |
-Sample preparation
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1 Details: THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS. STRUCTURES WERE CALCULATED IN THE PROGRAM ...Details: THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS. STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION ANGLE DYNAMICS. THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50 STRUCTURES WITH THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING SIMULATED ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE SELECTED TO REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS DISPLAYED NO NOE VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3 DEGREES. THE MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION OF THE COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY POWELL ENERGY MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: THE SELECTION UTILIZED THE LOWEST ENERGY STRUCTURES WITH NO NOE VIOLATIONS EXCEEDING 0.3 ANGSTROMS AND NO DIHEDRAL VIOLATIONS EXCEEDING 0.3 DEGREES. Conformers calculated total number: 100 / Conformers submitted total number: 25 |