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

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Basic information

Entry
Database: PDB / ID: 6dtz
TitleCrystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain, Y397F 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 / SAD / Resolution: 1.36 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 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0535
Polymers23,3471
Non-polymers7064
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.806, 50.810, 90.035
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: 23347.309 Da / Num. of mol.: 1 / Mutation: Y397F
Source method: isolated from a genetically manipulated source
Details: GPGS - expression tag remnant Y397F - mutation
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRI2, YKL045W, YKL258 / Production host: Escherichia coli (E. coli)
References: UniProt: P20457, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: 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
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.542 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.36→22.12 Å / Num. obs: 40483 / % possible obs: 98.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 9.31 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.72
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3282 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 3945 / CC1/2: 0.796 / % possible all: 97.87

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→22.12 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.76
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1998 4.94 %RANDOM
Rwork0.155 ---
obs0.157 40460 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.1 Å2 / Biso mean: 14.9677 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 1.36→22.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 32 158 1695
Biso mean--24.55 24.73 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.3940.26461440.23792648279298
1.394-1.43170.22971400.21062702284298
1.4317-1.47380.21911530.189227182871100
1.4738-1.52140.19441370.17412712284998
1.5214-1.57570.20691200.16422720284099
1.5757-1.63880.1891450.15042749289499
1.6388-1.71340.15171350.14627612896100
1.7134-1.80370.1861490.140727272876100
1.8037-1.91660.17121530.132627762929100
1.9166-2.06450.16871440.13642744288899
2.0645-2.27210.16611500.14062773292399
2.2721-2.60040.16241360.15222681281795
2.6004-3.27450.19371330.15842787292098
3.2745-22.12790.15921590.15472964312399
Refinement TLS params.Method: refined / Origin x: 4.2862 Å / Origin y: 24.8249 Å / Origin z: 14.4442 Å
111213212223313233
T0.041 Å2-0.0021 Å20.0019 Å2-0.0422 Å20.001 Å2--0.0691 Å2
L0.5153 °20.0303 °2-0.4565 °2-0.5916 °2-0.0906 °2--1.7964 °2
S-0.0097 Å °0.0363 Å °0.0156 Å °-0.0131 Å °-0.0025 Å °-0.0109 Å °0.0235 Å °-0.0189 Å °0.0114 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA316 - 512
2X-RAY DIFFRACTION1ALLA601 - 860

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