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- PDB-5of3: Crystal structure of the heterotrimeric PriSLX primase from S. so... -

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Basic information

Entry
Database: PDB / ID: 5of3
TitleCrystal structure of the heterotrimeric PriSLX primase from S. solfataricus.
Components
  • DNA primase large subunit PriL
  • DNA primase small subunit PriS
  • Uncharacterized protein
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 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 ...Primase X / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / DNA primase small subunit PriS / Primase X domain-containing protein / DNA primase large subunit PriL
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 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 10, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase small subunit PriS
B: DNA primase large subunit PriL
D: DNA primase small subunit PriS
E: DNA primase large subunit PriL
C: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,35116
Polymers182,9796
Non-polymers2,37110
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-58 kcal/mol
Surface area69060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.889, 104.889, 229.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein DNA primase small subunit PriS


Mass: 37643.895 Da / Num. of mol.: 2
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


Mass: 35788.969 Da / Num. of mol.: 2
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: priL, priB, SSO0557, C21_042 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9UWW1
#3: Protein Uncharacterized protein


Mass: 18056.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PriL
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0502 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q97ZS7

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Non-polymers , 3 types, 10 molecules

#4: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 11% PEG 8000, 21.5% ethylene glycol, 0.1 M bicine/Trizma base pH 8.5, 0.03 M di-, tri-, tetra- and penta-ethyleneglycol (Morpheus crystallization screen, Molecular Dimensions).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.906→46.91 Å / Num. obs: 54380 / % possible obs: 99.96 % / Redundancy: 9.3 % / Biso Wilson estimate: 89.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03641 / Rsym value: 0.1112 / Net I/σ(I): 15.09
Reflection shellResolution: 2.906→3.01 Å / Redundancy: 9 % / Rmerge(I) obs: 1.404 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 5392 / CC1/2: 0.527 / Rpim(I) all: 0.4952 / Rsym value: 1.489 / % possible all: 99.93

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Processing

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

1zt2


Resolution: 2.906→46.91 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 29.07
RfactorNum. reflection% reflection
Rfree0.2713 5281 4.9 %
Rwork0.2283 --
obs0.2305 54374 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.906→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11398 0 130 0 11528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611793
X-RAY DIFFRACTIONf_angle_d0.53415887
X-RAY DIFFRACTIONf_dihedral_angle_d13.517229
X-RAY DIFFRACTIONf_chiral_restr0.0421772
X-RAY DIFFRACTIONf_plane_restr0.0032035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9061-2.93920.32961390.31343302X-RAY DIFFRACTION99
2.9392-2.97370.35032020.30763473X-RAY DIFFRACTION100
2.9737-3.010.34551920.30423393X-RAY DIFFRACTION100
3.01-3.04810.32891740.30643434X-RAY DIFFRACTION100
3.0481-3.08820.32852000.31673371X-RAY DIFFRACTION100
3.0882-3.13050.4122020.34813343X-RAY DIFFRACTION100
3.1305-3.17520.39682200.37153413X-RAY DIFFRACTION100
3.1752-3.22260.43751300.33933458X-RAY DIFFRACTION100
3.2226-3.27290.34611920.31713384X-RAY DIFFRACTION100
3.2729-3.32660.33411560.2893434X-RAY DIFFRACTION100
3.3266-3.38390.27981260.26393545X-RAY DIFFRACTION100
3.3839-3.44540.29661600.25653354X-RAY DIFFRACTION100
3.4454-3.51170.39441660.26033457X-RAY DIFFRACTION100
3.5117-3.58330.29931780.25523355X-RAY DIFFRACTION100
3.5833-3.66120.30361880.2453465X-RAY DIFFRACTION100
3.6612-3.74640.26521820.23473447X-RAY DIFFRACTION100
3.7464-3.840.26521680.22913341X-RAY DIFFRACTION100
3.84-3.94380.28411820.21833443X-RAY DIFFRACTION100
3.9438-4.05980.2631760.21653403X-RAY DIFFRACTION100
4.0598-4.19070.22391780.22393437X-RAY DIFFRACTION100
4.1907-4.34040.27271420.20373485X-RAY DIFFRACTION100
4.3404-4.51410.2691680.20143440X-RAY DIFFRACTION100
4.5141-4.71940.22861500.19813370X-RAY DIFFRACTION100
4.7194-4.96790.2431800.19583486X-RAY DIFFRACTION100
4.9679-5.27880.27061960.20223384X-RAY DIFFRACTION100
5.2788-5.68580.24181720.21173396X-RAY DIFFRACTION100
5.6858-6.25680.32741690.22773400X-RAY DIFFRACTION100
6.2568-7.15960.24931600.22133453X-RAY DIFFRACTION100
7.1596-9.01040.25192320.19473350X-RAY DIFFRACTION100
9.0104-46.910.21812010.20993390X-RAY DIFFRACTION99

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