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- PDB-5o6e: Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4 -

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Basic information

Entry
Database: PDB / ID: 5o6e
TitleStructure of ScPif1 in complex with TTTGGGTT and ADP-AlF4
Components
  • ATP-dependent DNA helicase PIF1
  • DNA (5'-D(*TP*TP*TP*GP*GP*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 / mitochondrial genome maintenance / telomere maintenance via recombination / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / negative regulation of telomere maintenance via telomerase / DNA duplex unwinding ...telomerase inhibitor activity / G-quadruplex DNA unwinding / G-quadruplex DNA binding / mitochondrial genome maintenance / telomere maintenance via recombination / replication fork reversal / 5'-3' DNA helicase activity / double-strand break repair via break-induced replication / negative regulation of telomere maintenance via telomerase / DNA duplex unwinding / DNA unwinding involved in DNA replication / nuclear replication fork / 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 / DNA / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.345 Å
AuthorsLu, K.Y. / Chen, W.F. / Rety, S. / Liu, N.N. / Xu, X.G.
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 20, 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 1.2Jan 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: ATP-dependent DNA helicase PIF1
B: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')
D: DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,70511
Polymers127,5614
Non-polymers1,1447
Water0
1
A: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3706
Polymers63,7802
Non-polymers5904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area25830 Å2
MethodPISA
2
B: ATP-dependent DNA helicase PIF1
D: DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3355
Polymers63,7802
Non-polymers5543
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-28 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.605, 150.605, 136.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1004-

CL

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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 / Plasmid: PET15b-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): C2566H / References: UniProt: P07271, DNA helicase
#2: DNA chain DNA (5'-D(*TP*TP*TP*GP*GP*T)-3')


Mass: 2134.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 4 types, 7 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.44 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% PEG5000-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: 3.34→65.214 Å / Num. obs: 25042 / % possible obs: 92.65 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 17.23
Reflection shellResolution: 3.34→3.46 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 2024 / CC1/2: 0.86 / % possible all: 78.99

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O6B
Resolution: 3.345→65.214 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 1253 5.01 %5%
Rwork0.1784 ---
obs0.1822 24993 95.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.345→65.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 223 67 0 8456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018618
X-RAY DIFFRACTIONf_angle_d1.39211636
X-RAY DIFFRACTIONf_dihedral_angle_d16.9725286
X-RAY DIFFRACTIONf_chiral_restr0.0691287
X-RAY DIFFRACTIONf_plane_restr0.0081453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3447-3.47860.36711240.3012169X-RAY DIFFRACTION81
3.4786-3.63690.30911510.23842732X-RAY DIFFRACTION100
3.6369-3.82860.28641320.21552297X-RAY DIFFRACTION84
3.8286-4.06850.26171250.19752576X-RAY DIFFRACTION94
4.0685-4.38250.23631530.15572730X-RAY DIFFRACTION100
4.3825-4.82340.21241350.13812762X-RAY DIFFRACTION100
4.8234-5.52110.23871380.16182775X-RAY DIFFRACTION100
5.5211-6.95470.27041640.19282772X-RAY DIFFRACTION100
6.9547-65.22620.24441310.16162927X-RAY DIFFRACTION100

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