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- PDB-7otj: Crystal structure of Pif1 helicase from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7otj
TitleCrystal structure of Pif1 helicase from Candida albicans
Components
  • ATP-dependent DNA helicase PIF1
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
KeywordsHYDROLASE / Helicase Pif1
Function / homology
Function and homology information


: / : / : / telomerase inhibitor activity / G-quadruplex DNA binding / replication fork reversal / : / telomere maintenance via recombination / double-strand break repair via break-induced replication / negative regulation of telomere maintenance via telomerase ...: / : / : / telomerase inhibitor activity / G-quadruplex DNA binding / replication fork reversal / : / telomere maintenance via recombination / double-strand break repair via break-induced replication / negative regulation of telomere maintenance via telomerase / nuclear replication fork / 3'-5' exonuclease activity / telomere maintenance / DNA helicase activity / mitochondrial membrane / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA helicase / DNA replication / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
: / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold ...: / : / DNA helicase Pif1, 2B domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / PHOSPHATE ION / DNA / ATP-dependent DNA helicase PIF1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsRety, S. / Xi, X.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural study of the function of Candida Albicans Pif1.
Authors: Lu, K.Y. / Xin, B.G. / Zhang, T. / Liu, N.N. / Li, D. / Rety, S. / Xi, X.G.
History
DepositionJun 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase PIF1
B: ATP-dependent DNA helicase PIF1
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)122,33525
Polymers120,3604
Non-polymers1,97521
Water2,108117
1
A: ATP-dependent DNA helicase PIF1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,38816
Polymers60,1802
Non-polymers1,20814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-48 kcal/mol
Surface area21900 Å2
MethodPISA
2
B: ATP-dependent DNA helicase PIF1
D: DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9479
Polymers60,1802
Non-polymers7677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-42 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.973, 79.960, 94.110
Angle α, β, γ (deg.)90.000, 117.279, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

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


Mass: 58399.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q59RQ0, DNA helicase
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')


Mass: 1780.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Candida albicans (yeast)

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Non-polymers , 6 types, 138 molecules

#3: 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
#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: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl 0.1M pH 7.5 PEG 4K 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.575→82.51 Å / Num. obs: 40378 / % possible obs: 96.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.75 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.058 / Rrim(I) all: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 2.575→2.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2065 / CC1/2: 0.91 / Rpim(I) all: 0.278 / Rrim(I) all: 0.527 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSbuilt on 20170615data reduction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O6B

5o6b


Resolution: 2.58→82.51 Å / SU ML: 0.3619 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 27.892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2421 2072 5.14 %
Rwork0.2063 38243 -
obs0.2081 40315 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.81 Å2
Refinement stepCycle: LAST / Resolution: 2.58→82.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6919 210 101 117 7347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00377346
X-RAY DIFFRACTIONf_angle_d0.71049971
X-RAY DIFFRACTIONf_chiral_restr0.04551144
X-RAY DIFFRACTIONf_plane_restr0.00591221
X-RAY DIFFRACTIONf_dihedral_angle_d16.94922773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.640.35981170.27882598X-RAY DIFFRACTION99.41
2.64-2.70.33921430.2682608X-RAY DIFFRACTION99.14
2.7-2.770.31251450.25272605X-RAY DIFFRACTION98.99
2.77-2.860.28751360.23812641X-RAY DIFFRACTION99.46
2.86-2.950.29241460.23472607X-RAY DIFFRACTION99.46
2.95-3.050.27971410.24772607X-RAY DIFFRACTION99.78
3.05-3.180.31511500.25572594X-RAY DIFFRACTION99.6
3.18-3.320.28951420.23882622X-RAY DIFFRACTION99.5
3.32-3.490.27951040.22872188X-RAY DIFFRACTION82.15
3.5-3.710.28341180.22592277X-RAY DIFFRACTION86.52
3.71-40.23421360.20892355X-RAY DIFFRACTION88.87
4-4.40.19921490.16892598X-RAY DIFFRACTION99.21
4.4-5.040.19231400.15482627X-RAY DIFFRACTION98.68
5.04-6.350.21561600.19542636X-RAY DIFFRACTION99.15
6.35-82.50.19971450.18682680X-RAY DIFFRACTION97.95
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)
12.10654015340.485661317109-0.8641636725150.752180580445-0.4508445265923.71323563623-0.07396501644190.0529551827534-0.04314466489310.0626802215141-0.0291318664968-0.0389732925564-0.1182516169590.0965240771331-1.866538868E-50.47533301182-0.0422192793982-0.005387092978330.368006976547-0.01151446086370.49506979936913.75901377149.0419566564373.8298049679
21.813501000390.1473218026490.1954147900451.28877285711-0.2974163312921.18906637711-0.016638776753-0.248113712334-0.952478507506-0.05941147812020.0684704346079-0.07357560154630.3090865022970.183751935374-4.77165161875E-50.712834935011-0.0179826430886-0.07099872159940.6954352060830.1636926496780.9275212951136.79466271440.21473478984987.6100070316
33.503143951720.931001558218-0.6349318457131.18652675689-0.3979286857621.44010805793-0.00168308184496-0.181348406145-0.2925695372820.11802814831-0.152052039414-0.00215075237994-0.2066120167560.06720444010413.86970174133E-50.611352651338-0.05671860795160.003216590380570.397150404886-0.005234588691740.46446426216817.89795521179.2440060513185.4570175811
42.00768961120.41794927243-0.1818452810212.43857924913-0.5778824694513.988298934670.1294007923580.2710211665250.0524264017493-0.169331368084-0.166694909072-0.144304803707-0.146348947910.309813313343-7.88114220457E-50.4619806035140.0167001829722-0.0006348613596880.4715236127060.05967287453250.48962860142945.834705802944.975553021646.9592878743
52.68178971125-0.887933183722-0.01815097838741.47556314417-0.5475094621531.664646641110.155297583368-0.00940158220130.1128611382590.0392899891103-0.226442371141-0.280627227824-0.1319185160850.39323092041-0.007223278033460.545891483056-0.125993073727-0.04026946142090.6115853426270.05898714332480.50903802156349.550120454234.888724552870.5992572932
61.65111649428-0.5804444012760.1395554419052.8101166702-0.888578636912.580225528840.1381202798840.0801392141265-0.0461670405612-0.184963973104-0.166386536924-0.338160859178-0.05447430027140.455755849068-0.01332633691380.427740107063-0.0866988843394-0.02294336143130.542895150632-0.00216646601670.4914769363550.529928062334.378564548963.9347928156
70.4457289098220.1469407447060.1223954556360.543826050928-0.3979408540460.4076713932460.478250345702-0.432981103620.6652439019510.558400042254-0.164160618849-0.721041265013-0.527008949670.248563288128-0.0002817119970820.748087250687-0.181177882394-0.02909572982410.596573003914-0.03623887302120.58121501552323.974336535617.251081709182.2396078995
80.3659819489370.05893863345150.04090967014420.437102677768-0.3144952193230.2422397910160.589901374223-0.5274542994860.4723845316490.0178519166044-0.0594775187475-0.730540382417-0.6862372596070.89335022218-0.0008675816521820.597847462057-0.166127540423-0.05303826645250.9513963402760.02940186006620.65707497294656.818661127144.691092772963.3087143635
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 366 through 618 )AA366 - 6181 - 242
22chain 'A' and (resid 619 through 780 )AA619 - 780243 - 340
33chain 'A' and (resid 781 through 878 )AA781 - 878341 - 438
44chain 'B' and (resid 366 through 560 )BE366 - 5601 - 182
55chain 'B' and (resid 561 through 674 )BE561 - 674183 - 296
66chain 'B' and (resid 675 through 881 )BE675 - 881297 - 436
77chain 'C' and (resid 1 through 6 )CI1 - 6
88chain 'D' and (resid 1 through 6 )DJ1 - 6

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