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- PDB-8bnx: Crystal structure of Pif1 from Deferribacter desulfuricans in com... -

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Basic information

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


telomere maintenance / DNA helicase activity / DNA repair / metal ion binding
Similarity search - Function
: / DNA helicase Pif1, 2B domain / WYL domain profile. / WYL domain / WYL domain / : / DNA helicase Pif1-like / PIF1-like helicase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...: / DNA helicase Pif1, 2B domain / WYL domain profile. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AAA family ATPase
Similarity search - Component
Biological speciesDeferribacter desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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

Downloads & links

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Assembly

Deposited unit
A: AAA family ATPase
B: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0393
Polymers117,5322
Non-polymers5061
Water00
1
A: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2722
Polymers58,7661
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AAA family ATPase


Theoretical massNumber of molelcules
Total (without water)58,7661
Polymers58,7661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.797, 151.376, 51.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein AAA family ATPase


Mass: 58766.215 Da / Num. of mol.: 2
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 K-12 (bacteria) / References: UniProt: D3PAZ1
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tris-HCl 100mM 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: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.544→104.256 Å / Num. obs: 24905 / % possible obs: 93.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 97.02 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.058 / Rrim(I) all: 0.148 / Net I/σ(I): 8.3
Reflection shellResolution: 2.544→2.855 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1245 / CC1/2: 0.704 / Rpim(I) all: 0.456 / Rrim(I) all: 1.195 / % possible all: 62.8

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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: 3.12→71.9 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.9247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 982 4.69 %
Rwork0.2399 19970 -
obs0.2406 20952 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.65 Å2
Refinement stepCycle: LAST / Resolution: 3.12→71.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 31 0 6733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266872
X-RAY DIFFRACTIONf_angle_d0.67699291
X-RAY DIFFRACTIONf_chiral_restr0.05011069
X-RAY DIFFRACTIONf_plane_restr0.00731161
X-RAY DIFFRACTIONf_dihedral_angle_d7.3082887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.280.36451300.30462810X-RAY DIFFRACTION99.97
3.28-3.490.31661460.30082792X-RAY DIFFRACTION99.83
3.49-3.760.30061480.25642784X-RAY DIFFRACTION99.83
3.76-4.140.26031320.2542828X-RAY DIFFRACTION99.93
4.14-4.730.25581410.22542861X-RAY DIFFRACTION99.93
4.73-5.960.25781520.23292851X-RAY DIFFRACTION99.87
5.96-71.90.21061330.22143044X-RAY DIFFRACTION99.78
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)
12.52729912512-0.8670655936080.7569847551222.836636802150.8619662378723.54590787485-0.304531473727-0.105909434889-0.378282608679-0.0555510323645-0.2943130356061.55505364130.62698455410.1653866408350.3644795555441.14599675711-0.04927414399520.2903410880110.562425864213-0.2177808798971.3095512973429.3369511736-7.15918761472-5.89494387422
24.02753736626-2.298990747161.417296531215.62657913161-0.6384822077784.39890884602-0.2312109155980.446561677786-0.290814748858-0.2795540721320.2233806860590.6485155433580.06505619216310.2559748824730.05525638427190.4487505369470.0300367696592-0.02318807122550.640152412638-0.0008382549232160.45036731388831.844090724314.8073482241-10.4458005548
32.22363588464-0.2805791331480.6539186572084.07077570081-0.9419219876773.55551088639-0.208601705556-0.4306346264920.05562453426170.4064698210250.138219288085-0.06592159924550.4876986277330.04642061344760.09308863527110.5735003238180.204252383656-0.003318034699550.65584487903-0.08472022527240.50333040639638.763384031910.73503699853.1395501618
41.28624351262.166864509780.1649779030444.457991359630.9293092660260.598141028102-0.1839582234030.266778508725-2.13161594879-1.243449427560.5418058754560.735242393040.181206656339-0.0198525374501-0.2139074662070.4599993524130.09514101044540.05342666968931.1674735433-0.001891820776192.29847060213-2.7498759790325.6853472632-1.61739814699
53.2682605765-0.3688280624241.201971632660.6619191025140.4580986088552.747317818110.0885947500162-1.50411959153-1.785556636710.611027238667-0.2676301188240.336081174875-0.239163349783-1.286693491520.1795660269040.326397124634-0.03699097412310.04101302128621.715602525010.372882559011.57065022937-7.5686848700734.32728431899.52843231798
63.02835249671-1.652398129211.965388926973.2986545122-1.784215134634.829222039630.202213305321-0.0775298012866-0.0357978845997-0.110349607309-0.173966127904-0.0795394015301-0.574343717036-0.223045110233-0.01922065646020.7728601288920.08449187165010.09049141240760.505912618051-0.02721572635060.46933965140918.05862598144.076972449-0.511153506367
72.88985074702-1.08372107131.260301878141.018845889650.4374802810373.475281793990.187556995888-0.0530433548536-0.0858788769418-0.0342991711477-0.1064871843620.0872455905461-0.000913788026922-0.587900608912-0.08650401070610.5319077471010.114329036780.06158457110430.4768036613110.02038326110970.4932274326310.990251507740.0093652247-0.0692714608883
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 155 )AA2 - 1551 - 154
22chain 'A' and (resid 156 through 243 )AA156 - 243155 - 242
33chain 'A' and (resid 244 through 423 )AA244 - 423243 - 422
44chain 'B' and (resid 6 through 61 )BC6 - 611 - 56
55chain 'B' and (resid 62 through 189 )BC62 - 18957 - 174
66chain 'B' and (resid 190 through 294 )BC190 - 294175 - 279
77chain 'B' and (resid 295 through 423 )BC295 - 423280 - 408

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