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Yorodumi- PDB-7r3x: The crystal structure of the L439V variant of Pol2CORE in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r3x | ||||||
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Title | The crystal structure of the L439V variant of Pol2CORE in complex with DNA and an incoming nucleotide | ||||||
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 / 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: 2.46 Å | ||||||
Authors | Barbari, S.R. / Beach, A.K. / Markgren, J.G. / Parkash, V. / Johansson, E. / Shcherbakova, P.V. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels. Authors: Barbari, S.R. / Beach, A.K. / Markgren, J.G. / Parkash, V. / Moore, E.A. / Johansson, E. / Shcherbakova, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r3x.cif.gz | 507.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r3x.ent.gz | 408.5 KB | Display | PDB format |
PDBx/mmJSON format | 7r3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r3x_validation.pdf.gz | 877.9 KB | Display | wwPDB validaton report |
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Full document | 7r3x_full_validation.pdf.gz | 896.9 KB | Display | |
Data in XML | 7r3x_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 7r3x_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/7r3x ftp://data.pdbj.org/pub/pdb/validation_reports/r3/7r3x | HTTPS FTP |
-Related structure data
Related structure data | 7r3yC 4m8oS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 136596.016 Da / Num. of mol.: 1 / Mutation: L439V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / 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, 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: 4889.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 100 molecules
#4: Chemical | ChemComp-DTP / | ||||
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#5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-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: 2.87 Å3/Da / Density % sol: 57.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8 % PEG 20K , 150 mM NaAc, 0-1,5% Glycerol, 50 mM MES pH6.5 |
-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: 0.976254 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→45.78 Å / Num. obs: 61906 / % possible obs: 99.8 % / Redundancy: 4.25 % / Biso Wilson estimate: 56.4 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.944 / Net I/σ(I): 7.95 |
Reflection shell | Resolution: 2.46→2.65 Å / Redundancy: 4.25 % / Mean I/σ(I) obs: 0.97 / Num. unique obs: 12304 / CC1/2: 0.596 / Rrim(I) all: 0.944 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4m8o Resolution: 2.46→45.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 27.253 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.75 Å2 / Biso mean: 73.254 Å2 / Biso min: 29.82 Å2
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Refinement step | Cycle: final / Resolution: 2.46→45.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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