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- PDB-6s3e: Crystal structure of helicase Pif1 from Thermus oshimai in apo form -

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Basic information

Entry
Database: PDB / ID: 6s3e
TitleCrystal structure of helicase Pif1 from Thermus oshimai in apo form
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: 3.787 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


Theoretical massNumber of molelcules
Total (without water)100,8822
Polymers100,8822
Non-polymers00
Water00
1
A: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,4411
Polymers50,4411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PIF1 helicase


Theoretical massNumber of molelcules
Total (without water)50,4411
Polymers50,4411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.268, 59.408, 117.150
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88

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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: Sodium Hepes-MOPS 0.1M Ethylene glycol 1.25% PEG 4000 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: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.78→36.71 Å / Num. obs: 10098 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 133.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1414 / Rpim(I) all: 0.0576 / Rrim(I) all: 0.153 / Net I/σ(I): 12.2
Reflection shellResolution: 3.78→3.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.121 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 738 / CC1/2: 0.81 / Rpim(I) all: 0.453 / Rrim(I) all: 1.21 / % possible all: 70.4

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSNov 1, 2016, built on 20170215data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 3.787→36.71 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 525 5.2 %5%
Rwork0.2366 ---
obs0.2396 10098 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 171.72 Å2
Refinement stepCycle: LAST / Resolution: 3.787→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 0 0 7024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047191
X-RAY DIFFRACTIONf_angle_d1.0449759
X-RAY DIFFRACTIONf_dihedral_angle_d21.2372734
X-RAY DIFFRACTIONf_chiral_restr0.0571072
X-RAY DIFFRACTIONf_plane_restr0.0071275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7873-4.16840.3325950.28412167X-RAY DIFFRACTION88
4.1684-4.77130.33861500.26722435X-RAY DIFFRACTION100
4.7713-6.01040.30981450.27582444X-RAY DIFFRACTION100
6.0104-36.710.25791350.19562527X-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)
14.38770.333-0.77157.96361.16075.76280.2292-0.1522-0.4460.48680.0503-0.59370.4483-0.256-0.32791.064-0.066-0.30361.02330.03960.882-29.95292.526919.2783
25.6526-0.15951.53385.4216-4.48689.73721.1510.0466-0.8751-0.8991-2.58290.0503-0.29790.3321.00951.1278-0.2654-0.13291.12450.04091.5736-10.987525.664127.3858
32.2819-0.70712.13681.57171.21724.2684-0.26631.05580.951-0.7448-0.02140.1938-0.39040.36360.4521.5635-0.0801-0.04811.66350.28331.0229-17.136925.146-1.809
47.81387.36791.41118.5676-0.88156.46450.54810.67390.05780.0432-0.0963-0.445-0.70110.1441-0.17941.13670.26730.03042.1002-0.30651.3874-7.409413.2326-2.7316
52.95384.46182.56764.0472.8797.0801-0.09810.7101-0.03270.19510.3549-0.26640.2030.6434-0.01820.93320.1532-0.10660.83370.18441.1912-19.153415.62569.2908
65.1114.2859-3.11687.22180.62924.3751-0.5335-0.47791.05861.36421.3509-0.0712-0.1177-0.464-0.54880.7907-0.0296-0.32711.3563-0.12651.1974-23.238420.323829.3105
79.1563-1.47590.69280.2091-0.63942.24580.24443.7122.8967-0.3049-0.67762.4871-0.44270.7339-0.12172.36110.04360.00471.44690.26722.1119-64.4439-2.501234.9826
83.6907-0.48153.42082.53572.0315.833-1.6765-0.78682.8281-3.0494-2.1806-3.2526-1.88652.9619-1.81053.58250.87711.73622.36690.35552.4996-54.964-2.229641.0913
95.4509-0.8803-0.67731.0206-0.93663.74480.6219-0.48941.08511.10860.33180.1581-0.62350.8602-0.87931.8865-0.35880.56891.2296-0.50972.3188-61.6899-5.368957.1126
103.128-0.36061.23587.23893.31351.84840.47241.02870.3612-0.0025-0.41210.0967-0.7001-1.2986-0.39961.4743-0.09570.19191.3555-0.0460.9981-75.1317-20.223436.5052
118.11191.8011-1.54451.9353-1.9026.9879-0.30560.90740.5597-0.2256-0.6420.64072.16792.48320.36581.2920.02440.04790.9975-0.11951.0367-58.172-38.641240.8
12-0.78640.25980.41159.46777.75145.37180.0895-0.80620.5536-1.45590.2536-0.659-1.25120.0545-0.46061.183-0.06760.12451.7319-0.17291.1916-42.9091-22.197936.6393
136.57215.82531.88358.33264.60367.3537-0.01210.45180.81330.5625-0.07510.6096-0.64030.04250.03691.19950.0206-0.01511.20120.14871.1404-54.2067-23.302843.0815
147.4424-2.2998-4.38517.41471.92282.47790.37820.26561.15690.3228-0.3904-0.7543-0.9092-0.0371-0.22681.1492-0.0456-0.04381.47070.02861.3569-74.2368-21.813243.5979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 400 )
5X-RAY DIFFRACTION5chain 'A' and (resid 401 through 469 )
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 503 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 98 )
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 243 )
10X-RAY DIFFRACTION10chain 'B' and (resid 244 through 282 )
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 316 )
12X-RAY DIFFRACTION12chain 'B' and (resid 317 through 408 )
13X-RAY DIFFRACTION13chain 'B' and (resid 409 through 456 )
14X-RAY DIFFRACTION14chain 'B' and (resid 457 through 503 )

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