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Yorodumi- PDB-1huo: CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1huo | |||||||||
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Title | CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Arndt, J.W. / Gong, W. / Zhong, X. / Showalter, A.K. / Liu, J. / Lin, Z. / Paxson, C. / Tsai, M.-D. / Chan, M.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes. Authors: Arndt, J.W. / Gong, W. / Zhong, X. / Showalter, A.K. / Liu, J. / Dunlap, C.A. / Lin, Z. / Paxson, C. / Tsai, M.D. / Chan, M.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1huo.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1huo.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 1huo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1huo ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1huo | 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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-Components
-DNA chain , 2 types, 4 molecules TCPD
#1: DNA chain | Mass: 3398.235 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 2083.388 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) / Plasmid: PT17B / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 123 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.57 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% PEG 3350, 70mM lithium sulfate, 100mM MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 172244 / Num. obs: 27893 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.224 / % possible all: 82.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 172244 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 8 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |