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- PDB-4b08: Yeast DNA polymerase alpha, Selenomethionine protein -

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Basic information

Entry
Database: PDB / ID: 4b08
TitleYeast DNA polymerase alpha, Selenomethionine protein
ComponentsDNA POLYMERASE ALPHA CATALYTIC SUBUNIT A
KeywordsTRANSFERASE / DNA POLYMERASE / DNA REPLICATION
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
B family DNA polymerase, thumb domain, alpha/beta motif / B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / Alpha-Beta Plaits - #2820 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Helicase, Ruva Protein; domain 3 / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal ...B family DNA polymerase, thumb domain, alpha/beta motif / B family DNA polymerase, thumb domain, four helix bundle / Helicase, Ruva Protein; domain 3 - #100 / Alpha-Beta Plaits - #2820 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #730 / Helicase, Ruva Protein; domain 3 / DNA polymerase alpha catalytic subunit, N-terminal domain / DNA polymerase alpha, zinc finger domain superfamily / DNA Polymerase alpha zinc finger / DNA polymerase alpha subunit p180 N terminal / Zinc finger, DNA-directed DNA polymerase, family B, alpha / DNA polymerase alpha catalytic subunit, catalytic domain / Ribonuclease H-like motif / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Monooxygenase / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase alpha catalytic subunit A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.67 Å
AuthorsPerera, R.L. / Torella, R. / Klinge, S. / Kilkenny, M.L. / Maman, J.D. / Pellegrini, L.
CitationJournal: 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
DepositionJun 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)104,8451
Polymers104,8451
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.969, 127.447, 144.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein DNA POLYMERASE ALPHA CATALYTIC SUBUNIT A / DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\:PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE- ...DNA POLYMERASE I SUBUNIT A / DNA POLYMERASE ALPHA\:PRIMASE COMPLEX P180 SUBUNIT / DNA POLYMERASE-PRIMASE COMPLEX P180 SUBUNIT / POL ALPHA-PRIMASE COMPLEX P180 SUBUNIT


Mass: 104844.914 Da / Num. of mol.: 1 / Fragment: POLYMERASE DOMAIN, RESIDUES 349-1258
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE PROTEIN
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P13382, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 9.4 / Details: 0.1 M BICINE PH 8.0-9.4, 6-10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.67→73.97 Å / Num. obs: 39626 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Biso Wilson estimate: 45.86 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.9
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1078)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.67→65.8 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
Details: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. RESIDUES 677-679, 816-847, 1056-1062 1176-1185 AND 1129-1258 ARE DISORDERED AND NOT INCLUDED IN THE STRUCTURE. THE STRUCTURE WAS REFINED ...Details: FOR REFINEMENT, REFMAC, BUSTER AND PHENIX WERE USED. RESIDUES 677-679, 816-847, 1056-1062 1176-1185 AND 1129-1258 ARE DISORDERED AND NOT INCLUDED IN THE STRUCTURE. THE STRUCTURE WAS REFINED WITH RIDING HYDROGEN THE HYDROGENS OF THE LAST REFINEMENT RUN ARE INCLUDED.
RfactorNum. reflection% reflection
Rfree0.234 1986 5 %
Rwork0.1952 --
obs0.1972 39564 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.5 Å2
Refinement stepCycle: LAST / Resolution: 2.67→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6615 0 0 110 6725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026760
X-RAY DIFFRACTIONf_angle_d0.5739143
X-RAY DIFFRACTIONf_dihedral_angle_d12.3112607
X-RAY DIFFRACTIONf_chiral_restr0.0361041
X-RAY DIFFRACTIONf_plane_restr0.0021181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6663-2.73290.29221550.24292587X-RAY DIFFRACTION99
2.7329-2.80680.29421390.22032622X-RAY DIFFRACTION100
2.8068-2.88940.3061490.22082657X-RAY DIFFRACTION100
2.8894-2.98270.27811170.21422674X-RAY DIFFRACTION100
2.9827-3.08930.2741320.21582662X-RAY DIFFRACTION100
3.0893-3.2130.29151560.21762655X-RAY DIFFRACTION100
3.213-3.35920.29641240.22042685X-RAY DIFFRACTION100
3.3592-3.53630.26441180.20362686X-RAY DIFFRACTION100
3.5363-3.75780.26371420.19262664X-RAY DIFFRACTION100
3.7578-4.04790.18681390.18522687X-RAY DIFFRACTION100
4.0479-4.45520.19611580.16222674X-RAY DIFFRACTION100
4.4552-5.09970.18311410.15292716X-RAY DIFFRACTION100
5.0997-6.42420.22511370.20092772X-RAY DIFFRACTION100
6.4242-65.82340.21271790.20562837X-RAY DIFFRACTION100

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