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- PDB-6di6: Crystal structure of eukaryotic DNA primase large subunit iron-su... -

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Basic information

Entry
Database: PDB / ID: 6di6
TitleCrystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain
ComponentsDNA primase large subunit
KeywordsREPLICATION / DNA primase / p58 / iron-sulfur cluster / regulatory subunit
Function / homology
Function and homology information


alpha DNA polymerase:primase complex / primosome complex / DNA replication, synthesis of primer / 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 JAY291 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 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)23,9514
Polymers23,3631
Non-polymers5883
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.085, 50.769, 89.832
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: 23363.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae 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.: 182 / 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: 2.01 Å3/Da / Density % sol: 38.65 %
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: 1.0782 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: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.38→35 Å / Num. obs: 37530 / % possible obs: 95.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 10.75 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.044 / Rrim(I) all: 0.106 / Χ2: 0.857 / Net I/σ(I): 9.3 / Num. measured all: 206412
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.312 / Num. unique obs: 4040 / CC1/2: 0.962 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Χ2: 0.978 / % possible all: 76.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.97 Å31.94 Å
Translation4.97 Å31.94 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: 1.39→31.94 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 12.43
RfactorNum. reflection% reflection
Rfree0.146 1879 5.01 %
Rwork0.124 --
obs0.126 37485 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.43 Å2 / Biso mean: 16.05 Å2 / Biso min: 6.07 Å2
Refinement stepCycle: final / Resolution: 1.39→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 24 182 1718
Biso mean--25.41 30.53 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3879-1.42540.16031420.11142466260889
1.4254-1.46740.1381470.09752662280996
1.4674-1.51470.14241410.09322689283097
1.5147-1.56890.12841480.09232710285897
1.5689-1.63170.12311340.09432731286597
1.6317-1.7060.13951450.09462729287498
1.706-1.79590.12851590.1012699285896
1.7959-1.90840.11081270.10152689281696
1.9084-2.05570.14391320.10992837296999
2.0557-2.26250.13041610.11942772293399
2.2625-2.58980.14941520.13262845299799
2.5898-3.26240.15441360.14752779291596
3.2624-31.94580.16931550.15132998315399
Refinement TLS params.Method: refined / Origin x: 3.9382 Å / Origin y: 24.7295 Å / Origin z: 14.8192 Å
111213212223313233
T0.0504 Å2-0.0012 Å20.002 Å2-0.0499 Å20.0029 Å2--0.08 Å2
L0.7209 °20.0371 °2-0.3968 °2-0.8501 °20.0335 °2--1.8096 °2
S-0.0078 Å °0.0457 Å °0.018 Å °-0.0114 Å °-0.0044 Å °-0.001 Å °0.0271 Å °-0.0264 Å °0.0054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 512
2X-RAY DIFFRACTION1allA601 - 882

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