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- PDB-6s3h: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3h
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bp
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA repair
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 / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai JL-2 (bacteria)
Thermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
E: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,15910
Polymers105,0504
Non-polymers1,1096
Water8,935496
1
A: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0805
Polymers52,5252
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-29 kcal/mol
Surface area19090 Å2
MethodPISA
2
B: PIF1 helicase
E: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0805
Polymers52,5252
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.682, 200.130, 53.955
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 4 molecules ABDE

#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 JL-2 (bacteria) / Gene: Theos_1468 / Plasmid: plasmid / Details (production host): 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*T)-3')


Mass: 2084.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

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Non-polymers , 4 types, 502 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Hepes-MOPS 0.1M CaCl2 0.03M MgCl2 0.03M PEG 8000 10% Ethylene glycol 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.057→53.86 Å / Num. obs: 66828 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0682 / Rpim(I) all: 0.0338 / Rrim(I) all: 0.08108 / Net I/σ(I): 10.71
Reflection shellResolution: 2.057→2.131 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3774 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 5458 / CC1/2: 0.848 / Rpim(I) all: 0.2785 / Rrim(I) all: 0.4722 / % possible all: 79.35

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 2.06→29.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1995 2.99 %RANDOM
Rwork0.201 ---
obs0.201 66813 97 %-
Displacement parametersBiso mean: 56.27 Å2
Baniso -1Baniso -2Baniso -3
1-7.2829 Å20 Å2-2.4749 Å2
2---2.7674 Å20 Å2
3----4.5155 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.06→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 220 66 496 7550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.069860HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2519SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1209HARMONIC5
X-RAY DIFFRACTIONt_it7230HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion893SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8539SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.08 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2361 -2.84 %
Rwork0.229 1299 -
all0.2292 1337 -
obs--75.11 %
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)
11.4436-0.1106-0.36730.4213-0.25521.5288-0.0378-0.0583-0.1110.0674-0.02050.02940.170.06740.0584-0.1187-0.03210.0105-0.11720.0014-0.165814.0185-36.118173.1031
20.0418-0.93560.70084.28151.06231.0474-0.1386-0.24870.2088-0.07740.05830.0625-0.171-0.09030.0802-0.32410.078-0.086-0.1479-0.19520.10665.4847-89.050654.0412
31.87093.0497-0.42542.4422-2.146-0.05790.00480.0671-0.44780.05090.092-0.07260.5576-0.0113-0.0968-0.01050.0126-0.0151-0.02270.0786-0.028818.198-46.298175.3755
4-0.3646-3.0993.02160.75252.8750.36460.0084-0.0779-0.03640.07280.0120.0325-0.0709-0.0109-0.0205-0.0761-0.0716-0.0683-0.2955-0.16770.2110.6168-81.981760.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }

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