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Yorodumi- PDB-4fyd: Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fyd | ||||||
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Title | Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / DNA replication / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information Inhibition of replication initiation of damaged DNA by RB1/E2F1 / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / RNA-templated DNA biosynthetic process / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / premeiotic DNA replication / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / lagging strand elongation / mitotic DNA replication initiation / DNA synthesis involved in DNA repair / leading strand elongation / DNA replication origin binding / DNA replication initiation / replication fork / double-strand break repair / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / chromatin binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Perera, R.L. / Pellegrini, L. | ||||||
Citation | Journal: eLife / Year: 2013 Title: Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha Authors: Perera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / Pellegrini, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fyd.cif.gz | 697.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fyd.ent.gz | 568.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fyd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4fyd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4fyd_validation.xml.gz | 58.5 KB | Display | |
Data in CIF | 4fyd_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/4fyd ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fyd | HTTPS FTP |
-Related structure data
Related structure data | 4b08C 4fvmSC 4fxdC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 103401.703 Da / Num. of mol.: 2 / Fragment: Polymerase domain, UNP residues 349-1258 / Mutation: R508A, N509A, D998N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC17, N2181, POL1, YNL102W / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: P13382, DNA-directed DNA polymerase #2: DNA chain | Mass: 7627.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #3: DNA/RNA hybrid | Mass: 3929.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #4: Chemical | |
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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: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 0.2M MgAc2, 10% PEG8000, microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.39 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 97.34 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 3.1→3.26 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8380 / Rsym value: 0.974 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FVM Resolution: 3.1→48.801 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.08 / Stereochemistry target values: ML Details: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. THE STRUCTURE WAS REFINED WITH RIDING HYDROGENS. THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.801 Å
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Refine LS restraints |
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LS refinement shell |
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