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- PDB-6di2: Crystal structure of eukaryotic DNA primase large subunit iron-su... -

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Basic information

Entry
Database: PDB / ID: 6di2
TitleCrystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y397L mutant
ComponentsDNA primase large subunit
KeywordsREPLICATION / DNA primase / p58 / iron-sulfur cluster
Function / homology
Function and homology information


alpha DNA polymerase:primase complex / DNA replication, synthesis of primer / DNA replication initiation / 4 iron, 4 sulfur cluster binding / DNA binding / 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: 1.32 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
DepositionMay 22, 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

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Assembly

Deposited unit
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9014
Polymers23,3131
Non-polymers5883
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.950, 50.865, 89.620
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


Mass: 23313.291 Da / Num. of mol.: 1 / Mutation: Y397L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain JAY291) (yeast)
Strain: JAY291 / Gene: PRI2, C1Q_02024 / Production host: Escherichia coli (E. coli)
References: UniProt: C7GP29, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 38.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: MPD, TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0787 Å / Relative weight: 1
ReflectionResolution: 1.32→35 Å / Num. obs: 44491 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.26 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Χ2: 0.911 / Net I/σ(I): 11.7 / Num. measured all: 301921
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.184 / Num. unique obs: 4720 / CC1/2: 0.985 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 1.049 / % possible all: 94.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.96 Å33.62 Å
Translation4.96 Å33.62 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTZ

6dtz


Resolution: 1.32→33.62 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 11.08
RfactorNum. reflection% reflection
Rfree0.141 2126 4.79 %
Rwork0.12 --
obs0.121 44421 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.02 Å2 / Biso mean: 17.5 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.32→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 24 202 1727
Biso mean--23.14 29.62 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3213-1.3520.14611350.1062682281797
1.352-1.38590.13271480.094627972945100
1.3859-1.42330.12831390.085327872926100
1.4233-1.46520.11691330.082528062939100
1.4652-1.51250.12351390.085227932932100
1.5125-1.56660.11161390.079427742913100
1.5666-1.62930.12091540.079427992953100
1.6293-1.70340.10691220.084828162938100
1.7034-1.79320.11531500.091428152965100
1.7932-1.90560.1181460.097428132959100
1.9056-2.05270.13431540.105928432997100
2.0527-2.25920.14241460.112528162962100
2.2592-2.5860.15841440.134528683012100
2.586-3.25770.15581390.14522850298999
3.2577-33.63430.16051380.15623036317499

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