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- PDB-6du0: Crystal structure of eukaryotic DNA primase large subunit iron-su... -

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Basic information

Entry
Database: PDB / ID: 6du0
TitleCrystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y395L mutant
ComponentsDNA primase large subunit
KeywordsREPLICATION / DNA primase / p58 / iron-sulfur cluster / regulatory subunit
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / DNA replication, synthesis of primer / DNA replication initiation / double-strand break repair ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / DNA replication initiation / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / alpha DNA polymerase:primase complex / Activation of the pre-replicative complex / DNA replication, synthesis of primer / DNA replication initiation / double-strand break repair / nuclear envelope / 4 iron, 4 sulfur cluster binding / DNA replication / DNA binding / nucleus / metal ion binding
Similarity search - Function
DNA primase, large subunit, eukaryotic / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA primase large subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsSalay, L.E. / Chazin, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118089 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Yeast require redox switching in DNA primase.
Authors: O'Brien, E. / Salay, L.E. / Epum, E.A. / Friedman, K.L. / Chazin, W.J. / Barton, J.K.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9935
Polymers23,3131
Non-polymers6804
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.462, 50.830, 90.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA primase large subunit / DNA polymerase alpha:primase complex p58 subunit / Pol alpha-primase complex p58 subunit / DNA ...DNA polymerase alpha:primase complex p58 subunit / Pol alpha-primase complex p58 subunit / DNA primase 58 kDa subunit


Mass: 23313.291 Da / Num. of mol.: 1 / Mutation: Y395L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRI2, YKL045W, YKL258 / Production host: Escherichia coli (E. coli)
References: UniProt: P20457, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.86 Å3/Da / Density % sol: 34.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS 8.5, 40-60% MPD / PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. obs: 29372 / % possible obs: 95.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.099 / Χ2: 1.111 / Net I/σ(I): 10.7 / Num. measured all: 97436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.92.60.3826240.8760.2580.4621.08285.6
1.9-1.972.80.40727510.240.2810.4971.09190.4
1.97-2.0630.27328730.9650.180.3281.06792.5
2.06-2.173.20.23629330.9690.1510.2811.12796.2
2.17-2.313.50.30430020.3540.1880.3581.18598.1
2.31-2.483.60.16530310.9860.1020.1951.06998.5
2.48-2.733.70.13230370.990.080.1541.11598.5
2.73-3.133.70.09430230.9940.0580.1111.14198.6
3.13-3.943.50.06930560.9940.0430.0821.13898.9
3.94-303.50.0630420.9920.0380.0711.0798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.9 Å29.26 Å
Translation4.9 Å29.26 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0222refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTZ

6dtz


Resolution: 1.82→29.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.3544 / WRfactor Rwork: 0.3215 / FOM work R set: 0.4973 / SU B: 13.348 / SU ML: 0.32 / SU R Cruickshank DPI: 0.2038 / SU Rfree: 0.1889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3241 847 5.3 %RANDOM
Rwork0.2734 ---
obs0.276 15173 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.25 Å2 / Biso mean: 54.126 Å2 / Biso min: 30.33 Å2
Baniso -1Baniso -2Baniso -3
1-11.21 Å2-0 Å20 Å2
2---5.46 Å2-0 Å2
3----5.75 Å2
Refinement stepCycle: final / Resolution: 1.82→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 30 13 1474
Biso mean--65.87 49.68 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171300
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.6842028
X-RAY DIFFRACTIONr_angle_other_deg1.3131.6743024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69620.75979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15215244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4911511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
LS refinement shellResolution: 1.818→1.865 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 62 -
Rwork0.511 1010 -
all-1072 -
obs--91.7 %

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