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

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Basic information

Entry
Database: PDB / ID: 6dtv
TitleCrystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain Y395F mutant
ComponentsDNA primase large subunitPrimase
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 / metal ion binding / nucleus
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: 1.12 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

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Assembly

Deposited unit
A: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6374
Polymers23,0491
Non-polymers5883
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 50.873, 89.911
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 / Primase / 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: 23049.012 Da / Num. of mol.: 1
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-SF4 / IRON/SULFUR CLUSTER / 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 38.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: MPD, TRIS 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 72580 / % possible obs: 93.7 % / Redundancy: 5 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Χ2: 1.078 / Net I/σ(I): 14.6 / Num. measured all: 360511
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Num. unique obs: 7757 / CC1/2: 0.998 / Rpim(I) all: 0.018 / Rrim(I) all: 0.041 / Χ2: 1.017 / % possible all: 43.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.68 Å25.44 Å
Translation4.68 Å25.44 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
DENZOdata reduction
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTZ

6dtz


Resolution: 1.12→25.44 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.137 3739 5.16 %
Rwork0.125 68768 -
obs0.125 72507 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.79 Å2 / Biso mean: 20.02 Å2 / Biso min: 9.57 Å2
Refinement stepCycle: final / Resolution: 1.12→25.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 38 179 1718
Biso mean--20.89 30 -
Num. residues----184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1175-1.13160.1691140.20672103221782
1.1316-1.14650.20921290.17352512264197
1.1465-1.16220.16931570.15872458261599
1.1622-1.17880.17581220.14352536265898
1.1788-1.19640.13411180.133425612679100
1.1964-1.21510.15191360.132535267199
1.2151-1.2350.1291390.123525662705100
1.235-1.25630.15291320.125425462678100
1.2563-1.27920.15051450.118225562701100
1.2792-1.30380.14331360.111525492685100
1.3038-1.33040.14361460.108225462692100
1.3304-1.35930.14621450.110525592704100
1.3593-1.39090.15081390.109925492688100
1.3909-1.42570.111260.109725802706100
1.4257-1.46420.16081200.097826002720100
1.4642-1.50730.10041240.098225622686100
1.5073-1.5560.12481560.096225682724100
1.556-1.61160.11031470.097225652712100
1.6116-1.67610.11991460.096225792725100
1.6761-1.75240.11971400.102525862726100
1.7524-1.84470.12181530.106325782731100
1.8447-1.96030.11481360.114226132749100
1.9603-2.11150.12071470.111726052752100
2.1115-2.32390.12371520.116325962748100
2.3239-2.65990.16251580.12726332791100
2.6599-3.34990.15691500.138226532803100
3.3499-25.44310.14041260.16372474260088
Refinement TLS params.Method: refined / Origin x: 4.2594 Å / Origin y: 24.8225 Å / Origin z: 14.3152 Å
111213212223313233
T0.0732 Å2-0.0025 Å20.0039 Å2-0.079 Å20.0023 Å2--0.1022 Å2
L0.4401 °20.0158 °2-0.4309 °2-0.4005 °2-0.0903 °2--1.5672 °2
S-0.0096 Å °0.045 Å °0.0205 Å °-0.0191 Å °-0.0001 Å °-0.0048 Å °0.0256 Å °-0.0316 Å °0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 512
2X-RAY DIFFRACTION1allA601 - 879

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