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Yorodumi- PDB-4ptf: Ternary crystal structure of yeast DNA polymerase epsilon with te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ptf | ||||||
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Title | Ternary crystal structure of yeast DNA polymerase epsilon with template G | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / TRANSFERASE-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 / 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 / DNA replication proofreading / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å | ||||||
Authors | Jain, R. / Rajashankar, K.R. / Buku, A. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal Structure of Yeast DNA Polymerase epsilon Catalytic Domain. Authors: Jain, R. / Rajashankar, K.R. / Buku, A. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ptf.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ptf.ent.gz | 199.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ptf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ptf_validation.pdf.gz | 827.1 KB | Display | wwPDB validaton report |
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Full document | 4ptf_full_validation.pdf.gz | 866.7 KB | Display | |
Data in XML | 4ptf_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 4ptf_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/4ptf ftp://data.pdbj.org/pub/pdb/validation_reports/pt/4ptf | HTTPS FTP |
-Related structure data
Related structure data | 4m8oS 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: 137458.922 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 1-1187) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL2, DUN2, YNL262W, N0825 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21951, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 3502.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA strand |
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#3: DNA chain | Mass: 5067.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA strand |
-Non-polymers , 5 types, 154 molecules
#4: Chemical | ChemComp-DCP / | ||||||
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#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-EDO / | #8: 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: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG5000 MME, 25 mM magnesium acetate, 1% DMSO, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0032 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2009 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0032 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 34414 / Num. obs: 34036 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.52 / Num. unique all: 1431 / Rsym value: 0.34 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4M8O Resolution: 2.809→46.812 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 26.15 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.809→46.812 Å
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Refine LS restraints |
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LS refinement shell |
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