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Yorodumi- PDB-6qib: The crystal structure of Pol2CORE in complex with DNA and an inco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qib | |||||||||
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Title | The crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Pol epsilon / DNA / complex / Fe-S / P-domain | |||||||||
Function / homology | Function and homology information gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / 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 ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / 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 / nucleotide-excision repair, DNA gap filling / mitotic sister chromatid cohesion / DNA replication proofreading / 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 / double-stranded DNA binding / mitotic cell cycle / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mRNA binding / nucleotide 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: 2.8 Å | |||||||||
Authors | Parkash, V. / Johansson, E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ε. Authors: Ter Beek, J. / Parkash, V. / Bylund, G.O. / Osterman, P. / Sauer-Eriksson, A.E. / Johansson, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qib.cif.gz | 256.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qib.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qib_validation.pdf.gz | 862.3 KB | Display | wwPDB validaton report |
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Full document | 6qib_full_validation.pdf.gz | 891.4 KB | Display | |
Data in XML | 6qib_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 6qib_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/6qib ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qib | HTTPS FTP |
-Related structure data
Related structure data | 6h1vC 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: 137202.734 Da / Num. of mol.: 1 / Mutation: D290A, E292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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: 4889.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#4: Chemical | ChemComp-SF4 / |
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#5: Chemical | ChemComp-DTP / |
#6: Chemical | ChemComp-CA / |
-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: 57.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10mM Tris HCl pH8, 10mM CaCl2, 15% PEG8000 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 3, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.8→78.48 Å / Num. obs: 38251 / % possible obs: 98.5 % / Redundancy: 4.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.066 / Rrim(I) all: 0.143 / Net I/σ(I): 7.8 | ||||||||||||||||||||||||
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: 2.8→78.48 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.458 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.23 Å2 / Biso mean: 69.068 Å2 / Biso min: 27.13 Å2
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Refinement step | Cycle: final / Resolution: 2.8→78.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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