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- PDB-5o6b: Structure of ScPif1 in complex with GGGTTTT and ADP-AlF4 -

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Basic information

Entry
Database: PDB / ID: 5o6b
TitleStructure of ScPif1 in complex with GGGTTTT and ADP-AlF4
Components
  • ATP-dependent DNA helicase PIF1
  • DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')
KeywordsHYDROLASE / Helicase SF1 ssDNA ATP analog
Function / homology
Function and homology information


telomerase inhibitor activity / G-quadruplex DNA unwinding / G-quadruplex DNA binding / telomere maintenance via recombination / mitochondrial genome maintenance / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / DNA duplex unwinding / DNA unwinding involved in DNA replication ...telomerase inhibitor activity / G-quadruplex DNA unwinding / G-quadruplex DNA binding / telomere maintenance via recombination / mitochondrial genome maintenance / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / nuclear replication fork / negative regulation of telomere maintenance via telomerase / chromosome organization / DNA helicase activity / telomere maintenance / replication fork / mitochondrial membrane / single-stranded DNA binding / DNA helicase / DNA recombination / mitochondrial inner membrane / DNA replication / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
: / : / DNA helicase Pif1, 2B domain / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / PHOSPHATE ION / DNA / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.029 Å
AuthorsLu, K.Y. / Chen, W.F. / Rety, S. / Liu, N.N. / Xu, X.G.
Funding support China, France, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China11574252, 31370798 China
Northwest A &F University Startup FundingZ101021103 China
International Associated Laboratory Helicase-mediated G-quadruplex DNA unwinding and Genome Stability France
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase.
Authors: Lu, K.Y. / Chen, W.F. / Rety, S. / Liu, N.N. / Wu, W.Q. / Dai, Y.X. / Li, D. / Ma, H.Y. / Dou, S.X. / Xi, X.G.
History
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / pdbx_seq_map_depositor_info
Item: _audit_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
B: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')
D: DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,42311
Polymers128,2194
Non-polymers1,2047
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-58 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.246, 88.373, 187.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere ...DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere stability protein 1


Mass: 61645.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PIF1, TST1, YML061C, YM9958.01C / Production host: Escherichia coli (E. coli) / Variant (production host): C2566H / References: UniProt: P07271, DNA helicase
#2: DNA chain DNA (5'-D(*GP*GP*GP*TP*TP*T)-3')


Mass: 2463.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 5 types, 564 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.54 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M Tris-HCl 0.2M Na2SO4 15% EPEG5000-MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.03→58.71 Å / Num. obs: 80210 / % possible obs: 98.09 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 54.36 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.01
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 7015 / CC1/2: 0.74 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.029→58.707 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 3939 4.91 %5%
Rwork0.1926 ---
obs0.1947 80200 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.029→58.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8230 246 71 557 9104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088710
X-RAY DIFFRACTIONf_angle_d0.9911760
X-RAY DIFFRACTIONf_dihedral_angle_d18.0025328
X-RAY DIFFRACTIONf_chiral_restr0.0551300
X-RAY DIFFRACTIONf_plane_restr0.0061459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.029-2.05370.361070.27052281X-RAY DIFFRACTION83
2.0537-2.07970.31641290.25732384X-RAY DIFFRACTION88
2.0797-2.10710.30071530.24332487X-RAY DIFFRACTION91
2.1071-2.1360.29291290.23282573X-RAY DIFFRACTION95
2.136-2.16650.26591540.23072646X-RAY DIFFRACTION97
2.1665-2.19880.2851590.22272704X-RAY DIFFRACTION99
2.1988-2.23320.24511290.21792753X-RAY DIFFRACTION99
2.2332-2.26980.23351310.2112770X-RAY DIFFRACTION100
2.2698-2.30890.2691440.21622707X-RAY DIFFRACTION100
2.3089-2.35090.27371450.22092780X-RAY DIFFRACTION100
2.3509-2.39620.27461340.21822748X-RAY DIFFRACTION100
2.3962-2.44510.30521330.21182755X-RAY DIFFRACTION100
2.4451-2.49820.23791390.20912751X-RAY DIFFRACTION100
2.4982-2.55630.23951660.20052737X-RAY DIFFRACTION100
2.5563-2.62030.25711610.20752736X-RAY DIFFRACTION100
2.6203-2.69110.27561290.2012817X-RAY DIFFRACTION100
2.6911-2.77030.2891540.20922728X-RAY DIFFRACTION100
2.7703-2.85970.26771640.21012730X-RAY DIFFRACTION100
2.8597-2.96190.3281250.20012793X-RAY DIFFRACTION100
2.9619-3.08050.22411230.20452783X-RAY DIFFRACTION100
3.0805-3.22070.22971330.20772799X-RAY DIFFRACTION100
3.2207-3.39050.26631190.20012827X-RAY DIFFRACTION100
3.3905-3.60290.26011570.18582770X-RAY DIFFRACTION100
3.6029-3.8810.21271110.17282856X-RAY DIFFRACTION100
3.881-4.27150.21211560.16162791X-RAY DIFFRACTION100
4.2715-4.88930.18321680.14592806X-RAY DIFFRACTION100
4.8893-6.1590.20061520.18352870X-RAY DIFFRACTION100
6.159-58.73150.20611350.19212879X-RAY DIFFRACTION95

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