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- PDB-6s3o: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3o
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*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 / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.974 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 China31370798,11304252,11574252,31301632 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
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3234
Polymers55,8712
Non-polymers4522
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-32 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.012, 64.489, 144.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PIF1 helicase


Mass: 50440.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl 0.1M NaF 0.03M NaBr 0.03M NaI 0.03M MES 0.03M PEG 4K 10% Glycerol 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.974→32.24 Å / Num. obs: 35963 / % possible obs: 87.65 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 30.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1244 / Rpim(I) all: 0.0507 / Rrim(I) all: 0.1346 / Net I/σ(I): 14.81
Reflection shellResolution: 1.974→2.045 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.8255 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 3642 / CC1/2: 0.938 / Rpim(I) all: 0.3553 / Rrim(I) all: 0.9014 / % possible all: 90.28

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 1.974→32.24 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1815 5.05 %5%
Rwork0.1866 ---
obs0.1885 35915 87.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.974→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 141 28 414 4087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053770
X-RAY DIFFRACTIONf_angle_d0.7185150
X-RAY DIFFRACTIONf_dihedral_angle_d25.3031442
X-RAY DIFFRACTIONf_chiral_restr0.047567
X-RAY DIFFRACTIONf_plane_restr0.005644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9738-2.02720.37771430.31692708X-RAY DIFFRACTION93
2.0272-2.08680.395310.2814747X-RAY DIFFRACTION95
2.0868-2.15420.25631480.22912831X-RAY DIFFRACTION99
2.1542-2.23120.29631460.21962955X-RAY DIFFRACTION100
2.2312-2.32050.26691140.23142083X-RAY DIFFRACTION71
2.3205-2.42610.25111570.21282987X-RAY DIFFRACTION100
2.4261-2.5540.27591490.21942965X-RAY DIFFRACTION100
2.554-2.7140.2608970.20362109X-RAY DIFFRACTION70
2.714-2.92350.23221790.20362969X-RAY DIFFRACTION100
2.9235-3.21770.22371600.19133016X-RAY DIFFRACTION100
3.2177-3.68310.21731750.17032612X-RAY DIFFRACTION88
3.6831-4.63950.17741580.14352957X-RAY DIFFRACTION96
4.6395-44.33140.18591580.16883161X-RAY DIFFRACTION99
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)
11.2391-0.06150.33131.2743-0.14912.56320.0063-0.0409-0.07690.3547-0.07330.07770.3754-0.05590.06150.2726-0.03220.0540.1729-0.04210.1815-10.48962.2546-12.701
21.54860.01130.00722.2837-0.57662.42840.01780.1297-0.1380.0745-0.01650.30470.2482-0.1961-0.00280.1621-0.04680.0470.2061-0.05510.2055-17.3974.2735-23.6575
32.48711.61480.49231.26710.23440.94650.1994-0.17670.0570.5439-0.18340.0212-0.1318-0.01010.00390.3467-0.0156-0.01220.203-0.03730.2147-3.534719.9165-9.7676
40.7721-0.5803-0.93142.85841.34541.285-0.1570.07240.1384-0.03820.3502-0.6766-0.19470.5612-0.1630.2361-0.062-0.04940.3665-0.0640.349518.943917.1646-26.598
52.56-0.87440.23211.7695-0.27211.96470.05820.0862-0.06690.0396-0.0314-0.0822-0.05740.171-0.0140.1618-0.01-0.01010.1845-0.03610.18219.52431.3233-34.4602
60.227-0.3309-0.17142.47870.66511.80860.02490.0904-0.06490.0561-0.0569-0.01640.0322-0.1146-0.05260.1779-0.02590.00880.2284-0.03110.13732.081213.0069-31.5106
74.94511.17940.24932.94130.84761.5928-0.12660.0140.10860.2470.01820.2542-0.07980.0320.0560.2976-0.0141-0.01590.1525-0.03130.1604-2.357922.0235-14.7634
86.0491-0.53630.27060.0552-0.24996.6039-0.34070.55140.5192-0.60610.16890.3994-0.30130.00060.12420.1761-0.0218-0.04730.2856-0.01580.2029-0.906212.455-31.9422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 145 )
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 286 )
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 317 )
5X-RAY DIFFRACTION5chain 'A' and (resid 318 through 404 )
6X-RAY DIFFRACTION6chain 'A' and (resid 405 through 455 )
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 502 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 8 )

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