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

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Basic information

Entry
Database: PDB / ID: 7oar
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with parallel G-quadruplex
Components
  • DNA (28-MER)
  • Pif1 helicase
KeywordsHYDROLASE / Helicase Pif1 G-quadruplex
Function / homologyADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / DNA / DNA (> 10)
Function and homology information
Biological speciesThermus oshimai (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsDai, Y.X. / Liu, N.N. / Guo, H.L. / Chen, W.F. / Rety, S. / Xi, X.G.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870788, 11574252, 11774407 China
Centre National de la Recherche Scientifique (CNRS)LIA Helicase-mediated GquadruplexDNA unwinding and genome stability France
CitationJournal: Embo Rep. / Year: 2022
Title: Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.
Authors: Dai, Y.X. / Guo, H.L. / Liu, N.N. / Chen, W.F. / Ai, X. / Li, H.H. / Sun, B. / Hou, X.M. / Rety, S. / Xi, X.G.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70512
Polymers111,4783
Non-polymers1,2269
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-54 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.782, 151.782, 219.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein Pif1 helicase


Mass: 51200.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai (bacteria) / Plasmid: pET15b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain DNA (28-MER)


Mass: 9076.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 5 types, 47 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.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris 0.1M PEG 20000 10%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 2.58→131.447 Å / Num. obs: 877426 / % possible obs: 94.1 % / Redundancy: 19.7 % / Biso Wilson estimate: 87.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Rrim(I) all: 0.07 / Net I/σ(I): 26.8
Reflection shellResolution: 2.58→2.682 Å / Redundancy: 21.1 % / Rmerge(I) obs: 2.402 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 46926 / CC1/2: 0.651 / Rpim(I) all: 0.534 / Rrim(I) all: 2.461 / % possible all: 52.8

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Processing

Software
NameVersionClassification
PHENIXdev_3512refinement
PHENIXdev_3512refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3E

6s3e


Resolution: 2.58→37.39 Å / SU ML: 0.3546 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 2130 4.79 %
Rwork0.1944 42383 -
obs0.1967 44513 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.67 Å2
Refinement stepCycle: LAST / Resolution: 2.58→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 565 69 38 7528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00847713
X-RAY DIFFRACTIONf_angle_d1.149610599
X-RAY DIFFRACTIONf_chiral_restr0.05871163
X-RAY DIFFRACTIONf_plane_restr0.00741272
X-RAY DIFFRACTIONf_dihedral_angle_d24.04122959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.640.3426330.2929787X-RAY DIFFRACTION26.39
2.64-2.710.36781250.2762309X-RAY DIFFRACTION78.09
2.71-2.780.32631590.2682885X-RAY DIFFRACTION98.1
2.78-2.860.28041260.25933001X-RAY DIFFRACTION100
2.86-2.950.34111710.25542951X-RAY DIFFRACTION100
2.95-3.060.34731450.27142973X-RAY DIFFRACTION100
3.06-3.180.33581440.25162992X-RAY DIFFRACTION100
3.18-3.330.30571550.24492979X-RAY DIFFRACTION100
3.33-3.50.31421430.22553005X-RAY DIFFRACTION100
3.5-3.720.26431550.20413012X-RAY DIFFRACTION100
3.72-4.010.26671670.18563004X-RAY DIFFRACTION100
4.01-4.410.22341440.17053041X-RAY DIFFRACTION100
4.41-5.050.21421580.1543064X-RAY DIFFRACTION100
5.05-6.350.21681430.19563116X-RAY DIFFRACTION100
6.35-37.390.19661620.17793264X-RAY DIFFRACTION99.16
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)
12.65646766670.87640253585-0.2659108015372.83810348184-0.09275208934783.317647066270.000158312424607-0.1947865044460.08008348317920.3840427111690.0407062167013-1.40553201432-0.1773798795090.709654935324-0.09064498841640.8452450981730.0527458032024-0.222802920140.820597632057-0.1584468172121.3589850208268.4860628272-40.098660993-20.5330771176
22.505419126020.360470161431-0.6601765540815.258133333040.2602630639662.623346876960.190597031517-0.1240939990350.1816629688540.8870252698120.065840917536-0.60730709684-0.08463104615210.283769541756-0.2796482086570.854912748368-0.0318424704093-0.199390695730.510940134924-0.09019433815730.70537708474154.0581894861-30.6797891531-14.4034170656
33.46260676136-0.00786460625075-1.873166972443.053653923020.8822062895843.26955528722-0.370970558837-0.148576308353-0.2476810123850.9495706546430.223420967471-0.5827565222040.9015453249030.2958145361790.1042201043341.225130281690.0141722855405-0.1524891579210.61160424194-0.05529039362940.9945536586354.2780887181-62.1252204728-19.2687764251
41.8374491307-1.32675451758-0.2033043730042.38512357273-0.02829014015730.0448727344068-0.151465965901-0.792423606299-0.9291994937230.9706331523390.1831779376620.633404602413-0.1820129261450.127102194090.02634225290322.15405920769-0.10156393783-0.1117872284910.979317051051-0.009905645033330.99175649135346.5884065945-55.52249877719.0880593103
53.789735308870.155992243017-0.751259890791.9049262888-0.2173441149772.836854757590.543871726186-0.647933170238-0.02749219888831.15021899066-0.289328133916-0.4809203744760.5460563078840.282120210794-0.2606634608181.81261961364-0.204828094381-0.345181304250.816186102652-0.06618571685880.7709462064351.6085826317-43.40919279755.88840108739
61.99397238320.479388930103-1.30728200372.349846580731.342736096612.01978083721-0.17395235819-0.177843198059-0.09541104457010.768310035099-0.0202603139688-0.1474412909230.495650608595-0.119163677360.1760208716371.29242507441-0.0135830042681-0.2039329153550.6385349193320.01944842676090.75657964283848.3143679834-53.049488637-9.50138548939
76.09401860333-1.21432373266-1.351989484133.074966688121.124406658622.293559411430.09230092822061.255196078560.0710432749044-0.665937908729-0.167270310461-0.00538003131177-0.415383614988-1.049666274420.1155824594990.9354001877620.00615623983483-0.1512397374190.908732562409-0.04079659959260.72064805478948.1832001997-36.8879097277-30.3507853454
82.3292171643-1.074356939631.408634942464.25189127366-1.750486478643.235696902980.12439913294-0.0289189517239-0.135064251476-0.5280919660720.1736628257530.3680358568130.333582556386-0.197922278092-0.263644584150.664458840481-0.0361695574335-0.07586766463220.446240943185-0.05808347725320.53463321359846.02589258420.021330173016829.1686895154
92.8349613183-0.5060398336560.4432600864012.65603492914-0.5121155012721.58920883660.755748116503-1.117528168290.532083898764-0.4412868933650.1522252644641.399566082840.302407979889-1.08761415566-0.8357142162791.35942074723-0.418889199166-0.1699309665671.635063652870.1134695704721.9093572081627.1077233359-20.212194778435.7526632623
102.45913906771-0.845042908531.501424942735.30178356310.01508198324284.163462842250.259090801322-0.523192922843-0.499699639787-0.411489877007-0.01763135619680.5223652628281.04774876374-0.386972822045-0.2220425516090.770328201904-0.123955825616-0.1171328973080.494317520429-0.04939795151330.8357096450946.9920659297-13.057221348633.4459572654
111.51554479612-0.550852889709-0.3760567631522.090759980271.839170669872.95007730681-0.390242066182-0.9463919371120.1938718522691.1639800407-0.122129126022-0.0309360895942-0.4963720175860.02384090202140.435529438952.18869982903-0.185130859304-0.1747619633331.18975933979-0.2148215820170.93571811715448.9128091605-36.927568658511.3569214929
121.621577953981.63559275328-0.5162400075096.806848543411.240222724734.521917924130.1244848205010.68375304303-0.181462502011-2.196290132220.907671047888-0.9951293892910.6772832787780.640789912042-0.8867406700031.7946354243-0.0727655017359-0.2291795272091.09364548651-0.4067319615881.2582799981748.6902826542-21.182047097917.5140204167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 66 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 302 )
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 330 )
5X-RAY DIFFRACTION5chain 'A' and (resid 331 through 408 )
6X-RAY DIFFRACTION6chain 'A' and (resid 409 through 483 )
7X-RAY DIFFRACTION7chain 'A' and (resid 484 through 507 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 382 )
10X-RAY DIFFRACTION10chain 'B' and (resid 383 through 501 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 15 )
12X-RAY DIFFRACTION12chain 'C' and (resid 16 through 28 )

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