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Yorodumi- PDB-2fmp: DNA Polymerase beta with a terminated gapped DNA substrate and dd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fmp | ||||||
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Title | DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Nucleotidyl Transferase / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / 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 / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Batra, V.K. / Beard, W.A. / Shock, D.D. / Krahn, J.M. / Pedersen, L.C. / Wilson, S.H. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Authors: Batra, V.K. / Beard, W.A. / Shock, D.D. / Krahn, J.M. / Pedersen, L.C. / 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 | 2fmp.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fmp.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 2fmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fmp_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 2fmp_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 2fmp_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 2fmp_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fmp ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fmp | HTTPS FTP |
-Related structure data
Related structure data | 2fmqC 2fmsC 1bpyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 3 types, 3 molecules TPD
#1: DNA chain | Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 38241.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli) References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
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-Non-polymers , 4 types, 649 molecules
#5: Chemical | ChemComp-MG / | ||||
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#6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-DCT / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM HEPES, pH 7.5, 180 mM Sodium Acetate, 16 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 24, 2002 / Details: Osmic Mirrors |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→99 Å / Num. all: 50030 / Num. obs: 49071 / % possible obs: 96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.041 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.25 / Num. unique all: 50030 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1BPY Resolution: 1.65→17.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 976490.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5569 Å2 / ksol: 0.335502 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→17.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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