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Yorodumi- PDB-8b79: The crystal structure of M644G variant of DNA Pol Epsilon contain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b79 | |||||||||
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Title | The crystal structure of M644G variant of DNA Pol Epsilon containing UTP in the polymerase active site | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / protein-DNA complex | |||||||||
Function / homology | Function and homology information gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Model details | The ternary complex structure of M644G variant of DNA Pol Epsilon with an incoming ribonucleotide ...The ternary complex structure of M644G variant of DNA Pol Epsilon with an incoming ribonucleotide UTP and template DNA | |||||||||
Authors | Parkash, V. / Johansson, E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides. Authors: Parkash, V. / Kulkarni, Y. / Bylund, G.O. / Osterman, P. / Kamerlin, S.C.L. / Johansson, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b79.cif.gz | 495.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b79.ent.gz | 388.6 KB | Display | PDB format |
PDBx/mmJSON format | 8b79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/8b79 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/8b79 | HTTPS FTP |
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-Related structure data
Related structure data | 8b67C 8b6kC 8b76C 8b77C 8b7eC 4m8oS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 137101.453 Da / Num. of mol.: 2 / Fragment: Catalytic subunit of DNA Pol Epsilon / Mutation: M644G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL2, DUN2, YNL262W, N0825 / Plasmid: pET 28a / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P21951, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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-DNA chain , 2 types, 4 molecules CPDT
#2: DNA chain | Mass: 3293.174 Da / Num. of mol.: 2 / Fragment: DNA Template / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 22 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 55.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM MES, PEG20K,2.5% glycerol, 150mM Sodium Actetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97964 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2016 | |||||||||||||||||||||
Radiation | Monochromator: Si (111), double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97964 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.65→43.54 Å / Num. obs: 92708 / % possible obs: 99.8 % / Redundancy: 6.87 % / Biso Wilson estimate: 72.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.137 / Net I/σ(I): 9.89 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4m8o Resolution: 2.65→43.54 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML / Details: Phenix
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.23 Å2 / Biso mean: 75.9823 Å2 / Biso min: 34.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→43.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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