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Yorodumi- PDB-6g0a: The crystal structure of the Pol2 catalytic domain of DNA polymer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g0a | ||||||||||||
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Title | The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution. | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA / Pol2 / PolE / Epsilon / P301R / cancer | ||||||||||||
Function / homology | Function and homology information gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / Activation of the pre-replicative complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / Activation of the pre-replicative complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / Termination of translesion DNA synthesis / 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 / Dual incision in TC-NER / 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 / mitotic cell cycle / single-stranded DNA binding / 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: 2.62 Å | ||||||||||||
Authors | Parkash, V. / Johansson, E. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon. Authors: Parkash, V. / Kulkarni, Y. / Ter Beek, J. / Shcherbakova, P.V. / 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 | 6g0a.cif.gz | 253.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g0a.ent.gz | 191.7 KB | Display | PDB format |
PDBx/mmJSON format | 6g0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g0a_validation.pdf.gz | 822.9 KB | Display | wwPDB validaton report |
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Full document | 6g0a_full_validation.pdf.gz | 841.3 KB | Display | |
Data in XML | 6g0a_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 6g0a_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/6g0a ftp://data.pdbj.org/pub/pdb/validation_reports/g0/6g0a | HTTPS FTP |
-Related structure data
Related structure data | 6fwkC 6i8aC 4m8oS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 137235.672 Da / Num. of mol.: 1 / Mutation: P301R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: POL2, DUN2, YNL262W, N0825 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21951, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4599.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 19 molecules
#4: Chemical | ChemComp-DTP / | ||||
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#5: Chemical | #6: Chemical | ChemComp-FE / | #7: 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: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50mM MES pH 6.5, 150mM NaAc and 8% PEG20K / PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.62→78.78 Å / Num. obs: 44773 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 0.829 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.087 / Rrim(I) all: 0.156 / Net I/σ(I): 5.9 / Num. measured all: 136067 / Scaling rejects: 76 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4m8o Resolution: 2.62→19.977 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
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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 max: 112.3 Å2 / Biso mean: 53.9482 Å2 / Biso min: 20.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→19.977 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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