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Open data
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Basic information
Entry | Database: PDB / ID: 4fxd | ||||||
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Title | Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA | ||||||
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![]() | TRANSFERASE/DNA/RNA / DNA polymerase / DNA replication / TRANSFERASE-DNA-RNA complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / Pellegrini, L. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 659.8 KB | Display | ![]() |
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PDB format | ![]() | 540.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 496 KB | Display | ![]() |
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Full document | ![]() | 511.7 KB | Display | |
Data in XML | ![]() | 56.3 KB | Display | |
Data in CIF | ![]() | 76.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b08C ![]() 4fvmSC ![]() 4fydC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 103531.828 Da / Num. of mol.: 2 / Fragment: Polymerase domain, UNP residues 349-1258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CDC17, N2181, POL1, YNL102W / Plasmid: pRSFDuet-1 / Production host: ![]() ![]() #2: DNA chain | Mass: 4792.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #3: RNA chain | Mass: 3295.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Bicine, 12% PEG3350, 10 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 3→58.77 Å / Num. all: 45027 / Num. obs: 45027 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 91.64 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6546 / Rsym value: 0.921 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FVM Resolution: 3→55.526 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 34.05 / 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: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→55.526 Å
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Refine LS restraints |
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LS refinement shell |
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