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- PDB-5ofn: Crystal structure of the heterotrimeric PriSLX primase from S. so... -

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Basic information

Entry
Database: PDB / ID: 5ofn
TitleCrystal structure of the heterotrimeric PriSLX primase from S. solfataricus.
Components
  • DNA primase large subunit PriL,PriL-X fusion protein
  • DNA primase small subunit PriS
KeywordsREPLICATION / Primase / DNA-dependent RNA polymerase / DNA replication
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Primase X / Primase chain A, C-terminal domain / DNA primase large subunit PriL / DNA primase small subunit PriS / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal ...Primase X / Primase chain A, C-terminal domain / DNA primase large subunit PriL / DNA primase small subunit PriS / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit C-terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA primase small subunit PriS / DNA primase large subunit PriL
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsPellegrini, L. / Holzer, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust104641/Z/14/Z United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster.
Authors: Holzer, S. / Yan, J. / Kilkenny, M.L. / Bell, S.D. / Pellegrini, L.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 2024Group: 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 small subunit PriS
B: DNA primase large subunit PriL,PriL-X fusion protein
C: DNA primase large subunit PriL,PriL-X fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0574
Polymers113,9913
Non-polymers651
Water1267
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-11 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.052, 36.348, 110.941
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA primase small subunit PriS


Mass: 37643.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: priS, priA, SSO1048 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q97Z83, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA primase large subunit PriL,PriL-X fusion protein


Mass: 38173.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain B is an engineered polypeptide. It contains the PriL residues of a chimeric construct spanning amino acids 1 to 211 of PriL fused to amino acids 42 to 154 of PriX.
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea), (gene. exp.) Sulfolobus solfataricus (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: priL, priB, SSO0557, C21_042 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9UWW1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 3350, 200 mM CaCl2, 0.5% n-octyl-beta-D-glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.005→46.17 Å / Num. obs: 16582 / % possible obs: 98.63 % / Redundancy: 3.2 % / Biso Wilson estimate: 77 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1168 / Rpim(I) all: 0.07654 / Rsym value: 0.1402 / Net I/σ(I): 9.18
Reflection shellResolution: 3.005→3.113 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.8095 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1556 / CC1/2: 0.535 / Rpim(I) all: 0.5204 / Rsym value: 0.9655 / % possible all: 95.17

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZT2

1zt2


Resolution: 3.005→46.17 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 33.07
RfactorNum. reflection% reflection
Rfree0.2979 1488 4.97 %
Rwork0.2412 --
obs0.2439 16579 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.005→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5099 0 1 7 5107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015212
X-RAY DIFFRACTIONf_angle_d0.3747020
X-RAY DIFFRACTIONf_dihedral_angle_d11.9183179
X-RAY DIFFRACTIONf_chiral_restr0.04780
X-RAY DIFFRACTIONf_plane_restr0.002887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0053-3.10230.38751190.37032466X-RAY DIFFRACTION91
3.1023-3.21320.45231510.4012559X-RAY DIFFRACTION95
3.2132-3.34180.43191470.38382618X-RAY DIFFRACTION94
3.3418-3.49380.44781030.31782487X-RAY DIFFRACTION93
3.4938-3.6780.34461300.28532654X-RAY DIFFRACTION95
3.678-3.90830.32881380.26232631X-RAY DIFFRACTION97
3.9083-4.20990.33861410.23572633X-RAY DIFFRACTION96
4.2099-4.63330.24891540.19682592X-RAY DIFFRACTION95
4.6333-5.3030.26641400.19732629X-RAY DIFFRACTION95
5.303-6.67850.25361230.22032588X-RAY DIFFRACTION96
6.6785-46.170.2071420.18062579X-RAY DIFFRACTION94

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