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- PDB-7bil: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 7bil
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with oligo GGTTTGGTTTGGTT
Components
  • DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*GP*GP*TP*T)-3')
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / DNA repair / nucleotide binding / 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 / TETRAFLUOROALUMINATE ION / : / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai JL-2 (bacteria)
Thermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 China (NSFC)31370798,11304252,11574252, 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
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,61710
Polymers118,4693
Non-polymers1,1487
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-54 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.052, 103.438, 251.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1180-

HOH

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein PIF1 helicase


Mass: 57052.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai JL-2 (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): C2566H / References: UniProt: K7RJ88
#2: DNA chain DNA (5'-D(*GP*GP*TP*TP*TP*GP*GP*TP*TP*TP*GP*GP*TP*T)-3')


Mass: 4363.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

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Non-polymers , 5 types, 117 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-MG / MAGNESIUM ION


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


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Tris-HCl 0.1M NaF 0.03M NaI 0.03M NaBr 0.03M MES 0.03M PEG 4K 10%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.21→125.783 Å / Num. obs: 404851 / % possible obs: 99.58 % / Redundancy: 6.9 % / Biso Wilson estimate: 50.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 13.6
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 7 % / Rmerge(I) obs: 1.126 / Num. unique obs: 1459 / CC1/2: 0.812 / Rpim(I) all: 0.457 / Rrim(I) all: 1.217 / % possible all: 51

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
PHENIX1.18.2_3874+SVNrefinement
XDSBUILT 20200131data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3M

6s3m


Resolution: 2.21→44.02 Å / SU ML: 0.2436 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.7372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 2768 5.02 %
Rwork0.1791 52398 -
obs0.1812 55166 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.02 Å2
Refinement stepCycle: LAST / Resolution: 2.21→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 289 67 110 7474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01087562
X-RAY DIFFRACTIONf_angle_d1.38710336
X-RAY DIFFRACTIONf_chiral_restr0.0721133
X-RAY DIFFRACTIONf_plane_restr0.00841288
X-RAY DIFFRACTIONf_dihedral_angle_d22.71052884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.230.3093700.30161382X-RAY DIFFRACTION99.38
2.26-2.290.35411370.28142430X-RAY DIFFRACTION97.94
2.29-2.340.25631390.24182730X-RAY DIFFRACTION99.76
2.34-2.390.28241420.23462661X-RAY DIFFRACTION99.82
2.39-2.440.26321530.22132708X-RAY DIFFRACTION99.76
2.44-2.490.29011280.21362691X-RAY DIFFRACTION99.65
2.49-2.560.24511260.21372696X-RAY DIFFRACTION99.72
2.56-2.630.23631710.20142714X-RAY DIFFRACTION99.93
2.63-2.70.26761330.20622701X-RAY DIFFRACTION99.93
2.7-2.790.27171300.21422719X-RAY DIFFRACTION99.89
2.79-2.890.2711660.20222695X-RAY DIFFRACTION99.9
2.89-3.010.25021590.20512689X-RAY DIFFRACTION100
3.01-3.140.23161360.2062744X-RAY DIFFRACTION100
3.14-3.310.26471510.20412702X-RAY DIFFRACTION100
3.31-3.520.23841440.18912741X-RAY DIFFRACTION99.86
3.52-3.790.23361410.17722485X-RAY DIFFRACTION90.58
3.79-4.170.18431190.15882637X-RAY DIFFRACTION95.73
4.17-4.770.17181440.13872768X-RAY DIFFRACTION99.97
4.77-6.010.20851430.15552795X-RAY DIFFRACTION99.97
6.01-44.020.17671360.16162710X-RAY DIFFRACTION92.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4002259253-0.07322209942210.1248223614520.9891715706150.1962493489141.38659065929-0.0140344847226-0.1833111241590.3723186811880.06844090161280.0603937528579-0.0885306344764-0.03537321213710.100172107945-0.047008444960.274263803220.0289603259241-0.01544952455330.492139049297-0.08081125886320.44650353947627.80725766964.32680253677-50.8915659749
22.63927596625-0.04145228003091.047711819555.141460915110.5357311841623.29735992905-0.0461229413235-0.3520730054440.1667784982250.4454454720610.2620309918440.0169167768056-0.268165676807-0.46173707039-0.1805402812440.3830165546240.1229472404620.00439140769220.602001345663-0.007314206294020.38844827884322.0120913771-8.5943651578-30.4363913427
32.98502116993-0.487088788890.2128143237651.90803042202-0.7033865339892.404259952090.0612612355078-0.1679010165790.4670488239760.15677345819-0.0698771681420.0609415661133-0.2898141337-0.2002005871560.003067812872660.2902844980180.04965011745860.02016478087350.505084256455-0.1076555560260.48504905646913.35082875485.6204172471-48.0718786805
42.50364626513-0.1401876831050.1366158539673.57784436690.3061657375552.192961132770.146226165634-0.472190439256-0.5413725747840.6811526294430.1402678564610.01514949511320.642023166763-0.105544631691-0.2918932296340.7478560902210.0267210873774-0.1094390315990.4285421420410.07339470522240.4878820905940.1815593796-32.8938602268-10.1891495401
52.18000673891-1.09192659083-0.3942102390782.467961712361.56373624382.686717957450.130954351012-0.0702426030697-0.0189822667972-0.1282811411570.137656665344-0.278983272359-0.1598129884770.114455407325-0.2804642364220.5077676379290.0603728490117-0.03146143264440.42753307174-0.08782727861370.43819525816649.6141383766-17.648745266-21.7740748154
66.0331582373-3.742068274774.578469496753.49044368718-4.404123809655.107248791320.02128211381270.424840527529-0.3555867240950.416933581514-0.1466717501760.35764230580.136806994936-0.3444056173020.2109055297110.5819890293040.0461241282323-0.001110659531340.859337427348-0.1697889384090.50921244399233.3555917139-11.363308011-30.4978832808
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 67 through 302 )AA67 - 3021 - 236
22chain 'A' and (resid 303 through 421 )AA303 - 421237 - 355
33chain 'A' and (resid 422 through 502 )AA422 - 502356 - 436
44chain 'B' and (resid 67 through 260 )BE67 - 2601 - 194
55chain 'B' and (resid 261 through 502 )BE261 - 502195 - 436
66chain 'C' and (resid 1 through 14 )CI1 - 14

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