+Open data
-Basic information
Entry | Database: PDB / ID: 7k97 | ||||||
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Title | Human DNA polymerase beta dGDP product complex with Mn2+ | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Polymerase / nucleotide analog / DNA BINDING PROTEIN / 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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / 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 / 5'-deoxyribose-5-phosphate lyase activity / POLB-Dependent Long Patch Base Excision Repair / 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 / 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 / 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 / microtubule / in utero embryonic development / 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 / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Varela, F.A. / Freudenthal, B.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta. Authors: Varela, F.A. / Freudenthal, B.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k97.cif.gz | 210 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k97.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 7k97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/7k97 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/7k97 | HTTPS FTP |
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-Related structure data
Related structure data | 7k96C 2fmsS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37182.410 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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-DNA chain , 3 types, 3 molecules DPT
#2: DNA chain | Mass: 1536.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#3: DNA chain | Mass: 3390.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
#4: DNA chain | Mass: 4829.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 4 types, 67 molecules
#5: Chemical | ChemComp-MN / #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 50 mM imidazole, 350 mM sodium acetate, 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16511 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 36.2 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.093 / Χ2: 0.933 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 804 / CC1/2: 0.54 / CC star: 0.837 / Rpim(I) all: 0.517 / Rrim(I) all: 0.961 / Χ2: 0.99 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FMS Resolution: 2.4→30.58 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4916 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.40193329624 Å / Origin y: -9.45776770914 Å / Origin z: 13.1964007502 Å
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Refinement TLS group | Selection details: all |