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- PDB-8bnv: Crystal structure of Pif1 from Deferribacter desulfuricans in apo from -

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Basic information

Entry
Database: PDB / ID: 8bnv
TitleCrystal structure of Pif1 from Deferribacter desulfuricans in apo from
ComponentsAAA family ATPase
KeywordsHYDROLASE / Helicase Thermophile
Function / homology
Function and homology information


DNA helicase activity / telomere maintenance / DNA repair / metal ion binding
Similarity search - Function
: / DNA helicase Pif1, 2B domain / WYL domain / WYL domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...: / DNA helicase Pif1, 2B domain / WYL domain / WYL domain / : / 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 speciesDeferribacter desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsRety, S. / Chen, W.F. / Xi, X.G.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Microorganisms / Year: 2023
Title: Structural Studies of Pif1 Helicases from Thermophilic Bacteria.
Authors: Rety, S. / Zhang, Y. / Fu, W. / Wang, S. / Chen, W.F. / Xi, X.G.
History
DepositionNov 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8833
Polymers58,7661
Non-polymers1162
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-9 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.764, 147.053, 78.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein AAA family ATPase


Mass: 58766.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deferribacter desulfuricans (bacteria) / Strain: DSM 14783 / JCM 11476 / NBRC 101012 / SSM1 / Gene: DEFDS_0256 / Production host: Escherichia coli (E. coli) / References: UniProt: D3PAZ1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tris-HCl 100 mM PEG 8K 12% Isopropanol 5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97848 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.86→75.993 Å / Num. obs: 12146 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 72.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Net I/σ(I): 14.5
Reflection shellResolution: 2.86→2.91 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 595 / CC1/2: 0.872 / Rpim(I) all: 0.321 / Rrim(I) all: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 2.86→37.64 Å / SU ML: 0.447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 647 5.34 %
Rwork0.2021 11472 -
obs0.2046 12119 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.05 Å2
Refinement stepCycle: LAST / Resolution: 2.86→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 7 7 3091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723146
X-RAY DIFFRACTIONf_angle_d0.94844248
X-RAY DIFFRACTIONf_chiral_restr0.0532486
X-RAY DIFFRACTIONf_plane_restr0.0061532
X-RAY DIFFRACTIONf_dihedral_angle_d15.62731182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.080.5171920.31782287X-RAY DIFFRACTION100
3.08-3.390.31121320.26052265X-RAY DIFFRACTION99.92
3.39-3.880.26271450.23762256X-RAY DIFFRACTION99.09
3.88-4.890.211240.172295X-RAY DIFFRACTION99.34
4.89-37.640.21771540.1722369X-RAY DIFFRACTION99.53
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)
13.292017405220.0236318581677-0.9862403052424.902378264621.554489250198.2997777827-0.0649678678849-0.3550293741810.09633405953980.3317547523260.247847683783-0.0427768798128-0.2413382464380.222696684225-0.176532507910.2863742894830.02838397988240.03651535345270.3431705902290.02146290184860.39512747878837.210222916518.3384259812-4.20109981303
21.72947405432-3.4839553749-2.388876393299.523535611082.591025291755.2015329542-0.114650128316-0.2019870218110.954618028169-0.446121201381-0.0261976126667-1.6822810758-0.8225781605991.551583703050.3188439830940.98569363683-0.17821045202-0.322712263371.704601471820.01839469002871.8021469641941.746225851549.2593934181-5.11516447814
32.50081388965-2.164491837620.5706701876744.84199329148-0.6522546658792.15629593908-0.1809192953-0.3799790750230.1409143417710.109257430840.1233837615890.129035518133-0.57242133278-0.1270190902250.003407511757530.535963737599-0.000530909329449-0.01250921201370.6498242061450.06226448665780.44914046473222.783481357538.0422375859-11.6387924997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 177 )20 - 1771 - 147
22chain 'A' and (resid 178 through 221 )178 - 221148 - 191
33chain 'A' and (resid 222 through 411 )222 - 411192 - 381

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