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- PDB-9fb8: XChem refined PIF1-x0076 complex -

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Basic information

Entry
Database: PDB / ID: 9fb8
TitleXChem refined PIF1-x0076 complex
ComponentsATP-dependent DNA helicase PIF1
KeywordsDNA BINDING PROTEIN / Helicase / inhibitor / Complex / XChem
Function / homology
Function and homology information


protein-DNA-RNA complex disassembly / 5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / mitochondrial nucleoid / Telomere Extension By Telomerase ...protein-DNA-RNA complex disassembly / 5'-3' DNA/RNA helicase activity / telomerase inhibitor activity / G-quadruplex DNA binding / mitochondrial genome maintenance / single-stranded DNA helicase activity / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / mitochondrial nucleoid / Telomere Extension By Telomerase / telomere maintenance via telomerase / 5'-3' DNA helicase activity / DNA recombination / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / DNA repair / magnesium ion binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.727 Å
AuthorsBax, B.D. / Antson, A.A. / Sanders, C.M. / Brandao-Neto, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceLB19204 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure-based discovery of first inhibitors targeting the helicase activity of human PIF1.
Authors: Wever, M.J.A. / Scommegna, F.R. / Egea-Rodriguez, S. / Dehghani-Tafti, S. / Brandao-Neto, J. / Poisson, J.F. / Helfrich, I. / Antson, A.A. / Rodeschini, V. / Bax, B. / Roche, D. / Sanders, C.M.
History
DepositionMay 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6466
Polymers45,5711
Non-polymers1,0755
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-10 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.600, 143.714, 77.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1257-

HOH

21A-1263-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1 / PIF1/RRM3 DNA helicase-like protein


Mass: 45570.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIF1, C15orf20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H611, DNA helicase

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Non-polymers , 5 types, 378 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-O0J / N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide


Mass: 233.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: XChem 0.045uls compound (0.5M) in DMSO echo dispensed into crystal drop Drop = 0.3uls protein + 0.3us well +0.001uls seeds. Protein = 25uls 30mgs/ml human PIF1 (206-620) in 10mM Tris pH 7.5, ...Details: XChem 0.045uls compound (0.5M) in DMSO echo dispensed into crystal drop Drop = 0.3uls protein + 0.3us well +0.001uls seeds. Protein = 25uls 30mgs/ml human PIF1 (206-620) in 10mM Tris pH 7.5, 175mM NaCl, 2%glycerol, 5mM DTT, 0.1mM PMSF + 21uls 10mM Tris, 2.7uls 0.2M MgCl2, 5uls 100mM AMPPNP + 27uls H2O. Well = 4% Glycerol, 27% PEG 2KMME, 0.1M NaAcetate, 0.1M Tris pH8.5. Set up on douglas instruments robot - tray on ice - set-up room temperature - crystallised 4 degrees C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.727→27.83 Å / Num. obs: 43220 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 19.5
Reflection shellResolution: 1.73→1.77 Å / Num. unique obs: 3023 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.727→27.83 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.891 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2114 2134 4.94 %
Rwork0.1734 41061 -
all0.175 --
obs-43195 99.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.663 Å2
Baniso -1Baniso -2Baniso -3
1--2.208 Å20 Å2-0 Å2
2--0.903 Å20 Å2
3---1.304 Å2
Refinement stepCycle: LAST / Resolution: 1.727→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 68 373 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123362
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.8174578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.5916.36444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33510558
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.62210140
X-RAY DIFFRACTIONr_chiral_restr0.1220.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022548
X-RAY DIFFRACTIONr_nbd_refined0.230.21466
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22256
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2287
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.255
X-RAY DIFFRACTIONr_mcbond_it2.4792.7311710
X-RAY DIFFRACTIONr_mcangle_it3.3314.8992150
X-RAY DIFFRACTIONr_scbond_it4.1313.171652
X-RAY DIFFRACTIONr_scangle_it6.0155.6222424
X-RAY DIFFRACTIONr_lrange_it7.67735.51714425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.727-1.7720.2861590.2782888X-RAY DIFFRACTION96.1199
1.772-1.820.311590.2482882X-RAY DIFFRACTION99.9671
1.82-1.8730.2731480.222869X-RAY DIFFRACTION100
1.873-1.930.2591430.2162774X-RAY DIFFRACTION99.8973
1.93-1.9930.2531460.1972682X-RAY DIFFRACTION99.9647
1.993-2.0620.2141300.1772601X-RAY DIFFRACTION100
2.062-2.140.2671240.1782502X-RAY DIFFRACTION100
2.14-2.2270.1931200.1672428X-RAY DIFFRACTION100
2.227-2.3250.1971210.1692341X-RAY DIFFRACTION99.9594
2.325-2.4380.245960.1832240X-RAY DIFFRACTION100
2.438-2.5680.2341110.1842107X-RAY DIFFRACTION100
2.568-2.7230.2221040.1822028X-RAY DIFFRACTION100
2.723-2.9090.2141050.1771872X-RAY DIFFRACTION99.9494
2.909-3.1390.2181040.1751774X-RAY DIFFRACTION100
3.139-3.4340.221830.1631628X-RAY DIFFRACTION99.8832
3.434-3.8320.161770.1571494X-RAY DIFFRACTION99.6827
3.832-4.4110.169730.131326X-RAY DIFFRACTION100
4.411-5.3690.184670.1451136X-RAY DIFFRACTION100
5.369-7.4560.239480.184909X-RAY DIFFRACTION99.8956
7.456-27.830.13160.177580X-RAY DIFFRACTION100

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