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- PDB-8xak: Structure of Pif1-G4 complex -

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Basic information

Entry
Database: PDB / ID: 8xak
TitleStructure of Pif1-G4 complex
Components
  • ATP-dependent DNA helicase PIF1
  • DNA (34-MER)
KeywordsHYDROLASE/DNA / Pif1 / HYDROLASE / HYDROLASE-DNA complex
Function / homologyADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / DNA / DNA (> 10) / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHong, Z. / Song, H.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other government Singapore
CitationJournal: Nat Commun / Year: 2024
Title: Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge.
Authors: Hong, Z. / Byrd, A.K. / Gao, J. / Das, P. / Tan, V.Q. / Malone, E.G. / Osei, B. / Marecki, J.C. / Protacio, R.U. / Wahls, W.P. / Raney, K.D. / Song, H.
History
DepositionDec 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
C: ATP-dependent DNA helicase PIF1
D: DNA (34-MER)
B: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,12316
Polymers144,7794
Non-polymers1,34412
Water00
1
A: ATP-dependent DNA helicase PIF1
B: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0618
Polymers72,3902
Non-polymers6726
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-24 kcal/mol
Surface area28470 Å2
MethodPISA
2
C: ATP-dependent DNA helicase PIF1
D: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0618
Polymers72,3902
Non-polymers6726
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-30 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.163, 125.141, 258.233
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / DNA chain , 2 types, 4 molecules ACDB

#1: Protein ATP-dependent DNA helicase PIF1


Mass: 61691.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PIF1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BX49
#2: DNA chain DNA (34-MER) / AT11


Mass: 10697.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 12 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

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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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.9, 22.5 %(w/v) PEG 400, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→48 Å / Num. obs: 22444 / % possible obs: 99.35 % / Redundancy: 1.9 % / CC1/2: 0.904 / Net I/σ(I): 3.05
Reflection shellResolution: 3.5→3.625 Å / Num. unique obs: 2168 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3235 1999 8.91 %
Rwork0.2823 --
obs0.2859 22444 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7900 1400 72 0 9372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049715
X-RAY DIFFRACTIONf_angle_d1.06113388
X-RAY DIFFRACTIONf_dihedral_angle_d23.5941760
X-RAY DIFFRACTIONf_chiral_restr0.0541482
X-RAY DIFFRACTIONf_plane_restr0.0071471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.37851320.32321402X-RAY DIFFRACTION97
3.59-3.680.38291430.33291404X-RAY DIFFRACTION98
3.68-3.790.36591450.31171478X-RAY DIFFRACTION100
3.79-3.920.35131390.30821436X-RAY DIFFRACTION100
3.92-4.060.35321500.29241496X-RAY DIFFRACTION100
4.06-4.220.33191430.28161433X-RAY DIFFRACTION100
4.22-4.410.29961460.27621448X-RAY DIFFRACTION100
4.41-4.640.32491370.26541499X-RAY DIFFRACTION100
4.64-4.930.32571430.26071469X-RAY DIFFRACTION100
4.93-5.310.3211430.2661468X-RAY DIFFRACTION100
5.31-5.850.27851420.27421469X-RAY DIFFRACTION100
5.85-6.690.31271420.29331473X-RAY DIFFRACTION100
6.69-8.420.30931510.26911481X-RAY DIFFRACTION100
8.42-480.26861430.25191489X-RAY DIFFRACTION98

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