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- PDB-6s3n: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -

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Basic information

Entry
Database: PDB / ID: 6s3n
TitleCrystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-VO4
Components
  • (DNA (5'-D(P*TP*TP*TP*TP*TP*T)- ...) x 2
  • PIF1 helicase
KeywordsHYDROLASE / DNA helicase
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / 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 / VANADATE ION / DNA / DNA (> 10) / PIF1 helicase
Similarity search - Component
Biological speciesThermus oshimai (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.533 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
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,90110
Polymers111,7684
Non-polymers1,1336
Water63135
1
A: PIF1 helicase
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4385
Polymers55,8712
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-36 kcal/mol
Surface area19310 Å2
MethodPISA
2
B: PIF1 helicase
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4635
Polymers55,8962
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-35 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.093, 102.955, 249.697
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-1116-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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DNA (5'-D(P*TP*TP*TP*TP*TP*T)- ... , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*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: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 5455.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria)

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Non-polymers , 4 types, 41 molecules

#4: 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
#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: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Osdium Hepes-MOPS 0.1M NaF 0.03M NaI 0.03M NaBr 0.03M PEG 4K 20% Glycerol 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 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: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.533→44.05 Å / Num. obs: 36510 / % possible obs: 95.51 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 55.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1217 / Rpim(I) all: 0.0493 / Rrim(I) all: 0.1315 / Net I/σ(I): 10.44
Reflection shellResolution: 2.533→2.624 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.7295 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3756 / CC1/2: 0.929 / Rpim(I) all: 0.2652 / Rrim(I) all: 0.7838 / Χ2: 0.929 / % possible all: 99.71

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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: 2.533→44.047 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1782 4.89 %5%
Rwork0.1982 ---
obs0.201 36464 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.533→44.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 208 66 35 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037466
X-RAY DIFFRACTIONf_angle_d0.77310184
X-RAY DIFFRACTIONf_dihedral_angle_d24.2462846
X-RAY DIFFRACTIONf_chiral_restr0.0461122
X-RAY DIFFRACTIONf_plane_restr0.0051284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5335-2.6020.32881500.28232759X-RAY DIFFRACTION100
2.602-2.67850.37141100.28852026X-RAY DIFFRACTION74
2.6785-2.7650.38271250.27362703X-RAY DIFFRACTION98
2.765-2.86380.32471550.2642761X-RAY DIFFRACTION100
2.8638-2.97840.35111500.24412732X-RAY DIFFRACTION100
2.9784-3.11390.27951260.24372784X-RAY DIFFRACTION100
3.1139-3.2780.29211360.23442786X-RAY DIFFRACTION100
3.278-3.48330.30311030.23032201X-RAY DIFFRACTION79
3.4833-3.75220.24621480.20622557X-RAY DIFFRACTION92
3.7522-4.12950.25171450.1912770X-RAY DIFFRACTION100
4.1295-4.72640.21821640.15372812X-RAY DIFFRACTION100
4.7264-5.95250.22541330.17262841X-RAY DIFFRACTION100
5.9525-44.05310.20671370.16832950X-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)
10.77040.1158-0.9020.5101-0.08581.474-0.01040.30130.1072-0.0013-0.0023-0.13460.06870.0556-00.46980.0282-0.0160.7032-0.02140.540729.855-1.2233-59.956
20.8373-0.4053-0.14661.2893-0.38771.02970.0362-0.52250.04890.44590.0156-0.5180.18410.4186-00.47750.0628-0.07310.7262-0.10520.718440.91240.6785-40.261
30.9191-0.54090.73742.02060.22250.8403-0.03610.1390.3038-0.04670.0354-0.0848-0.13240.154600.45620.0054-0.0170.6405-0.08860.544135.09216.5391-48.045
40.8553-0.4793-0.17520.76170.56830.4207-0.0303-0.03040.5718-0.0323-0.0044-0.1885-0.354-0.30100.52620.002-0.02140.6404-0.06860.734331.076115.0338-47.0816
52.3395-0.18380.76331.51910.13662.9801-0.03430.24660.1936-0.09550.17720.20660.0333-0.1557-00.46720.0335-0.00150.6145-0.04420.58624.90781.5301-53.8694
62.1084-0.61580.47211.9612-0.04571.65040.0215-0.24340.03550.250.1004-0.10020.0699-0.1362-00.55290.01320.01360.6100.517420.39-8.5856-32.0367
73.007-1.0377-0.55391.0240.05072.53210.1165-0.07010.47040.1574-0.2252-0.0219-0.41080.0073-00.48550.0689-0.02240.5852-0.0370.613413.71319.7606-49.8356
80.48740.04350.0850.4669-0.22950.2010.0219-0.6795-0.49990.83930.23950.02150.62260.4618-01.18440.2036-0.1650.76240.07490.62445.4537-30.66130.8319
91.8771-0.357-0.32670.92540.30551.8185-0.068-0.3891-0.57660.37180.19330.04550.614-0.078300.93310.0678-0.09410.50530.07530.737541.6026-39.0646-16.5
102.0838-0.94250.61291.09320.06990.93150.1207-0.3598-0.47060.54090.10290.4542-0.002-0.62070.00010.8958-0.05270.02550.55750.08370.648432.734-30.773-12.4639
110.79780.17020.25832.22721.24341.71970.0908-0.66130.54530.16940.1527-0.1103-0.18830.174-00.77410.0945-0.08220.6631-0.17290.677847.6057-5.6831-7.9506
121.44920.0522-0.63122.57880.96951.85230.0787-0.1892-0.119-0.1060.187-0.2808-0.46090.291800.73510.0070.00790.6355-0.12080.733959.0877-21.1192-30.1726
131.5-1.1889-0.66851.9760.93852.26350.04610.1261-0.06580.00050.1756-0.22750.16480.0161-00.67620.0349-0.04290.5573-0.11210.601951.0727-26.106-27.4659
140.7977-1.22490.22322.99020.44172.1221-0.2355-0.25770.2010.2870.36180.515-0.0138-0.3129-00.78320.0664-0.05880.63280.01250.67538.1045-13.1968-11.4595
150.59340.59450.06690.7376-0.23730.6594-0.603-0.66660.62520.99140.0732-0.34610.0534-0.051300.78050.1058-0.11290.8639-0.02380.606822.81091.4071-34.9002
160.71320.60440.27820.52070.32630.8438-0.06591.1397-0.2907-0.2437-0.43370.149-0.10890.351200.78630.0047-0.13330.6022-0.02080.695344.7962-24.3633-25.8325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 221 )
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 303 )
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 446 )
7X-RAY DIFFRACTION7chain 'A' and (resid 447 through 502 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 193 )
10X-RAY DIFFRACTION10chain 'B' and (resid 194 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 303 )
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 374 )
13X-RAY DIFFRACTION13chain 'B' and (resid 375 through 446 )
14X-RAY DIFFRACTION14chain 'B' and (resid 447 through 502 )
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 8 )
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 8 )

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