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- PDB-7ada: Crystal structure of helicase Pif1 from Thermus oshimai mutant Q1... -

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Basic information

Entry
Database: PDB / ID: 7ada
TitleCrystal structure of helicase Pif1 from Thermus oshimai mutant Q164C-E409C
ComponentsPIF1 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
Biological speciesThermus oshimai JL-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 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 China (NSFC)31370798,11304252,11574252,31301632 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
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)101,2082
Polymers101,2082
Non-polymers00
Water00
1
A: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,6041
Polymers50,6041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,6041
Polymers50,6041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.070, 58.679, 118.155
Angle α, β, γ (deg.)90.000, 92.208, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein PIF1 helicase


Mass: 50604.141 Da / Num. of mol.: 2 / Mutation: Q164C, E409C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus oshimai JL-2 (bacteria) / Gene: Theos_1468
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K7RJ88
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Sodium Hepes-MOPS (pH 7.5) 0.03 M CaCl2 0.03 M MgCl2 10% PEG8000 20% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 3.34→52.55 Å / Num. obs: 15002 / % possible obs: 99.58 % / Redundancy: 6.9 % / Biso Wilson estimate: 138.11 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0492 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.05357 / Net I/σ(I): 24.54
Reflection shellResolution: 3.34→3.46 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.5995 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 1501 / CC1/2: 0.922 / CC star: 0.979 / Rpim(I) all: 0.2415 / Rrim(I) all: 0.647 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSMar 15, 2019, built on 20191211data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3E

6s3e


Resolution: 3.34→52.55 Å / SU ML: 0.5092 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.7776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3016 754 5.04 %
Rwork0.2447 14220 -
obs0.2477 14974 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.27 Å2
Refinement stepCycle: LAST / Resolution: 3.34→52.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6996 0 0 0 6996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047162
X-RAY DIFFRACTIONf_angle_d0.87679718
X-RAY DIFFRACTIONf_chiral_restr0.04791070
X-RAY DIFFRACTIONf_plane_restr0.00481266
X-RAY DIFFRACTIONf_dihedral_angle_d20.23492720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.60.45161410.36792821X-RAY DIFFRACTION99.66
3.6-3.960.41551460.31762823X-RAY DIFFRACTION99.46
3.96-4.530.31541740.27912797X-RAY DIFFRACTION99.6
4.53-5.710.36951500.25482859X-RAY DIFFRACTION99.9
5.71-52.550.2241430.20012920X-RAY DIFFRACTION99.45
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)
10.459529685542-0.1973239997080.4176335848040.6819087699370.1169745555960.860257242473-0.5849637533030.2415092209440.2976975323440.3574776808330.477230436296-0.264875872203-0.2858117690262.40487792270.003508545940191.455304169660.351010391295-0.1792611656831.670169919340.1413535547661.33528385857-14.4084632859-0.20547190735919.5845160526
21.66044753982-0.1395357100211.855489986713.161067817470.422295898951.995631880540.156748686324-0.392459071333-0.0230640348719-0.6337133243350.2514049308950.3009879199330.412514589226-0.3901904576272.62764331352E-51.21897164369-0.0695368355573-0.1791018701481.116737757220.1438342540820.901160362811-34.49901244010.97649465373714.6236386942
31.03869188099-0.847078826987-0.4148754399961.254914974641.386845055622.019354111140.171724074297-0.162454440998-0.83053415739-0.1800074597480.796056921010.1422100055551.02406310687-0.709652438072-0.0001208848964011.50272619053-0.236834296625-0.3625544373881.145494539610.238253958551.42445036636-30.66556129973.703145557222.0624665946
40.2907954362690.5553110556260.08462160135010.759789411039-0.008240904648150.009866060016860.155520140059-0.633926597025-0.3962853030790.1725421094210.04356870410010.3683086609840.328560173932-0.354895792839.76741278208E-51.30772346328-0.0292279288362-0.1517756832291.428056518790.01939953824251.21442722356-26.126724056111.151430539926.8683058653
51.915719958540.516027705330.0512677208411.354788130711.072879218380.904964802792-0.3660991837610.2312799818951.47044325760.146747069551-0.354895857836-0.312445368857-0.537845847413-0.343342612456-0.001041951216151.07161303954-0.0100002384198-0.1316760879361.099505523550.08566075445441.35795415387-12.795262708331.98099947622.1164925409
60.581108219736-0.366226739302-0.2031153255510.323066021441-0.01325045153560.234113989781-0.690997886311.24036438580.0426916778667-1.518165285260.498872005643-0.2591518937350.01531359796290.3911910765950.0006039900176441.52250752974-0.212594585111-0.2267356777861.869616842390.06082026327961.37470371191-18.147239679326.0870517761-6.26806790885
70.04995286608780.27202707097-0.1503292173671.28437587119-1.14851427170.888436098105-0.204122077530.440964016585-0.598647802942-0.5542648255120.342570896484-0.911123872710.829780605050.2775827095710.0001709716874791.318886683630.1592096181360.140631454611.97379876038-0.1310622574661.5447385295-9.9280283295216.7900139519-3.30484207049
80.135576014830.5907602680110.3997852338740.5536426317760.6151076500571.10923945059-0.1906772176960.1130427901860.10941239277-1.23386083217-0.510066355478-1.588301313870.5430121843460.4754642235590.001273973186691.5811241455-0.1162526711130.02936736672621.69552416516-0.0160938750331.19912800549-22.5342629433.749194753320.651350953429
90.4941716786010.5167543987330.02365431044260.4584621438540.2119676836831.62469780012-0.408625554253-0.330823665502-0.00184373039883-0.6623793291530.5074913333490.3566997781050.279133657746-0.170898629225-3.59585587746E-51.26000433972-0.0124721801630.1411724236051.272736430620.06930188770011.51823096921-17.136919102328.419046095618.261068811
100.356374001455-0.0758001794984-0.4225506323670.4137916846850.2205063908130.5206241304230.182775216505-3.067484291010.08562006365120.758804640190.54584310105-1.11732883153-0.1137650622080.1862568735070.03721361481621.46374367793-0.111952944759-0.4010885386041.227767225770.2307547570781.16647003013-25.141375285611.297649229734.1625687022
110.2572458217510.193308588783-0.08296283609760.633574932367-0.6745500722610.710114125592-0.3394262038242.576403813250.062668284584-1.01784754738-0.2251201135911.547971323970.0528814691721-2.333024418180.002939648381911.988376807130.305106662331-0.2837088504172.099115931110.3676903455042.23789009909-65.3379688312-1.2512066389136.0254602838
124.3903411088-1.789160897352.480658068111.572879570880.2806449211512.41454108678-0.1540896397930.2165485485210.428851711250.5547990645260.348051148853-0.429531438438-0.09191661252360.6525237463230.0003137227271461.48435114416-0.2697832445470.4710047656350.863222693916-0.3452372300761.84327975941-59.9839894524-4.0312887563254.9046409727
130.0514499816231-0.316817477225-0.4348186588710.8947466285141.234841290931.154899417820.199458747010.4404128659780.158071287420.82729131914-0.6213300827420.8125764768630.788260073915-1.5559298904-0.001104738069691.61117094642-0.1590216660160.03124883913711.62032242678-0.01504164383512.07742349634-71.8960261678-9.2325354605543.9776475911
143.66334477083-0.135726013451.08873738432.607390609740.2389856887970.290146525222-0.000391550714788-0.302060465750.283679213321-0.06257178077570.0730448873347-0.2925746597920.1431279821640.526091469929-0.003720502790391.10107803508-0.01043785629560.05811276421991.36093741508-0.1803288596520.931601311046-51.0410786676-24.786829978138.9031031409
151.503126961420.3562729657441.510906105282.112275243381.254306264361.65562397471-0.1296687851890.1272065536090.4342063105330.123862280639-0.09577638445770.4347193478470.13762538826-0.430364307267-0.0002412308833371.037469126530.01106523120370.1013062725520.988552740563-0.05106139308891.42745857619-70.8733112174-23.962722249443.9566226913
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 67 through 107 )AA67 - 1071 - 41
22chain 'A' and (resid 108 through 190 )AA108 - 19042 - 124
33chain 'A' and (resid 191 through 220 )AA191 - 220125 - 154
44chain 'A' and (resid 221 through 260 )AA221 - 260155 - 194
55chain 'A' and (resid 261 through 302 )AA261 - 302195 - 236
66chain 'A' and (resid 303 through 330 )AA303 - 330237 - 264
77chain 'A' and (resid 331 through 393 )AA331 - 393265 - 327
88chain 'A' and (resid 394 through 430 )AA394 - 430328 - 364
99chain 'A' and (resid 431 through 483 )AA431 - 483365 - 417
1010chain 'A' and (resid 484 through 502 )AA484 - 502418 - 436
1111chain 'B' and (resid 67 through 96 )BB67 - 961 - 30
1212chain 'B' and (resid 97 through 229 )BB97 - 22931 - 163
1313chain 'B' and (resid 230 through 260 )BB230 - 260164 - 194
1414chain 'B' and (resid 261 through 430 )BB261 - 430195 - 364
1515chain 'B' and (resid 431 through 502 )BB431 - 502365 - 436

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