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- PDB-6s3i: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3i
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-MgF4
Components
  • DNA (5'-D(P*TP*TP*TP*TP*T)-3')
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / nucleotide binding / DNA repair / metal ion binding
Similarity search - Function
: / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROMAGNESATE(2-) / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å
AuthorsDai, Y.X. / Chen, W.F. / Teng, F.Y. / Liu, N.N. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370798,11304252,11574252,31301632 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.
Authors: Dai, Y.X. / Chen, W.F. / Liu, N.N. / Teng, F.Y. / Guo, H.L. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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: PIF1 helicase
C: DNA (5'-D(P*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2065
Polymers54,6552
Non-polymers5523
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.195, 61.195, 260.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein PIF1 helicase


Mass: 50440.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*T)-3')


Mass: 4213.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

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Non-polymers , 4 types, 18 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F4Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES-imidazole 0.1M PEG 4000 8% Ethylene glycol 1.25% Glycerol 16%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.455→59.57 Å / Num. obs: 17618 / % possible obs: 9.31 % / Redundancy: 12.3 % / Biso Wilson estimate: 63.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08393 / Rpim(I) all: 0.02506 / Rrim(I) all: 0.08774 / Net I/σ(I): 19.04
Reflection shellResolution: 2.455→2.543 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.089 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 1836 / CC1/2: 0.794 / Rpim(I) all: 0.303 / Rrim(I) all: 1.131 / % possible all: 99.14

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 2.455→59.57 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.11
RfactorNum. reflection% reflectionSelection details
Rfree0.3015 913 5.18 %5%
Rwork0.2439 ---
obs0.247 17628 92.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.455→59.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 100 33 15 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043710
X-RAY DIFFRACTIONf_angle_d0.8495060
X-RAY DIFFRACTIONf_dihedral_angle_d20.9971414
X-RAY DIFFRACTIONf_chiral_restr0.045558
X-RAY DIFFRACTIONf_plane_restr0.005638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4547-2.58410.39971450.32552461X-RAY DIFFRACTION99
2.5841-2.7460.4354880.33311610X-RAY DIFFRACTION64
2.746-2.9580.34431270.31752516X-RAY DIFFRACTION99
2.958-3.25570.41021290.31022552X-RAY DIFFRACTION99
3.2557-3.72670.33211290.26632243X-RAY DIFFRACTION87
3.7267-4.6950.29651320.2112550X-RAY DIFFRACTION97
4.695-59.58910.24071630.21222783X-RAY DIFFRACTION100

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