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- PDB-6s3m: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3m
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-AlF4
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*G)-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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 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
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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(P*TP*TP*TP*TP*TP*G)-3')
D: DNA (5'-D(P*TP*TP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,90210
Polymers111,7934
Non-polymers1,1096
Water4,414245
1
A: PIF1 helicase
C: DNA (5'-D(P*TP*TP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4515
Polymers55,8962
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-28 kcal/mol
Surface area19680 Å2
MethodPISA
2
B: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4515
Polymers55,8962
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-27 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.735, 101.974, 250.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1121-

HOH

21A-1231-

HOH

31A-1236-

HOH

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein PIF1 helicase


Mass: 50440.816 Da / Num. of mol.: 2
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(P*TP*TP*TP*TP*TP*G)-3')


Mass: 5455.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

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Non-polymers , 4 types, 251 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 6.5
Details: MES-imidazole 0.1M PEG 4K 8% Ethylene glycol 1.25% Glycerol 16%

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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: 2.113→43.54 Å / Num. obs: 60373 / % possible obs: 93.17 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 40.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09505 / Rpim(I) all: 0.0391 / Rrim(I) all: 0.1029 / Net I/σ(I): 12.97
Reflection shellResolution: 2.113→2.189 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.7881 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6394 / CC1/2: 0.83 / Rpim(I) all: 0.3133 / Rrim(I) all: 0.8486 / % possible all: 100

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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: 2.113→43.54 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 30.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 2904 4.81 %5%
Rwork0.2242 ---
obs0.2263 60352 93.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.113→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 208 66 245 7527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077467
X-RAY DIFFRACTIONf_angle_d0.88910184
X-RAY DIFFRACTIONf_dihedral_angle_d22.1322846
X-RAY DIFFRACTIONf_chiral_restr0.0531120
X-RAY DIFFRACTIONf_plane_restr0.0061284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.113-2.14760.34331620.3152883X-RAY DIFFRACTION100
2.1476-2.18470.37091380.31222915X-RAY DIFFRACTION100
2.1847-2.22440.36361620.31482878X-RAY DIFFRACTION100
2.2244-2.26720.4678740.38421782X-RAY DIFFRACTION61
2.2672-2.31350.36411420.29342939X-RAY DIFFRACTION100
2.3135-2.36380.31651350.28232866X-RAY DIFFRACTION100
2.3638-2.41880.31981280.27792943X-RAY DIFFRACTION100
2.4188-2.47930.32271380.27222931X-RAY DIFFRACTION100
2.4793-2.54630.34461390.28682878X-RAY DIFFRACTION100
2.5463-2.62120.35521520.28442919X-RAY DIFFRACTION100
2.6212-2.70580.3289730.31621354X-RAY DIFFRACTION46
2.7058-2.80250.31951470.26892918X-RAY DIFFRACTION100
2.8025-2.91480.28561480.25842937X-RAY DIFFRACTION100
2.9148-3.04740.29271310.25772925X-RAY DIFFRACTION100
3.0474-3.20810.30031580.25232935X-RAY DIFFRACTION100
3.2081-3.40910.27271600.23352911X-RAY DIFFRACTION100
3.4091-3.67230.26691350.21161991X-RAY DIFFRACTION75
3.6723-4.04180.21691130.19862528X-RAY DIFFRACTION87
4.0418-4.62650.25371470.16572969X-RAY DIFFRACTION100
4.6265-5.82840.22421620.17882995X-RAY DIFFRACTION100
5.8284-66.54030.19811600.18333051X-RAY DIFFRACTION98
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)
11.7501-0.0929-0.35760.92020.32320.9348-0.06370.00290.21430.0430.0721-0.0642-0.03050.0961-0.06970.26520.0188-0.01780.3823-0.05960.332627.71763.8819-50.7805
22.0954-0.69450.22742.0355-0.51931.9851-0.096-0.21990.01220.3370.13210.0439-0.1022-0.15950.01150.38390.04560.00110.3689-0.02890.31221.7969-9.0053-30.1854
32.1777-0.416-0.54971.1162-0.55442.3050.0099-0.05730.220.1336-0.05830.1075-0.3137-0.27020.01490.28590.0387-0.02210.4147-0.09650.341713.33495.2427-47.99
41.8261-0.170.24582.15270.75481.9345-0.0235-0.405-0.33370.55550.1507-0.04450.42240.0523-0.16070.6360.0865-0.0240.4128-0.02890.417741.462-27.8237-10.2734
52.6465-0.3894-0.39731.70220.5012.5680.19220.00990.2822-0.0340.0459-0.103-0.26360.3457-0.30960.49860.06170.00210.4425-0.15110.493457.8337-20.4982-31.083
61.9869-0.6991-0.71451.84440.88812.19160.09420.1366-0.0394-0.00020.1653-0.0862-0.02570.2067-0.20140.45090.0833-0.0460.3532-0.13020.378850.8987-23.081-26.0061
71.5450.112-0.56083.6213-1.3993.01320.0858-0.07480.38550.21440.25150.49210.00530.0236-0.36750.61910.06180.02130.3738-0.25190.463636.4196-13.9844-9.5156
84.63911.63322.51334.3495-3.33186.0661-0.3265-0.82610.97170.94750.1387-0.6418-0.3138-0.23190.45740.43280.0757-0.08580.8073-0.19720.473322.72141.4986-35.2477
92.8793-0.2683-2.95137.03551.39313.27380.32140.3667-0.2857-0.2751-0.36390.4198-0.2925-0.35840.2560.56270.0854-0.08390.5566-0.16270.498444.5252-24.1695-25.7976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 303 )
2X-RAY DIFFRACTION2chain 'A' and (resid 304 through 422 )
3X-RAY DIFFRACTION3chain 'A' and (resid 423 through 502 )
4X-RAY DIFFRACTION4chain 'B' and (resid 68 through 303 )
5X-RAY DIFFRACTION5chain 'B' and (resid 304 through 367 )
6X-RAY DIFFRACTION6chain 'B' and (resid 368 through 462 )
7X-RAY DIFFRACTION7chain 'B' and (resid 463 through 502 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 8 )
9X-RAY DIFFRACTION9chain 'D' and (resid 3 through 8 )

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