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- PDB-5fhf: Crystal structure of Bacteroides sp Pif1 in complex with ADP-AlF4 -

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Basic information

Entry
Database: PDB / ID: 5fhf
TitleCrystal structure of Bacteroides sp Pif1 in complex with ADP-AlF4
ComponentsUncharacterized protein
KeywordsHYDROLASE / Pif1 helicase / DNA helicase
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / DNA repair / nucleotide binding
Similarity search - Function
DNA helicase Pif1-like / PIF1-like helicase / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / UvrD_C_2 domain-containing protein / UvrD_C_2 domain-containing protein
Similarity search - Component
Biological speciesBacteroides sp. 2_1_16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsZhou, X. / Ren, W. / Bharath, S.R. / Song, H.
CitationJournal: Cell Rep / Year: 2016
Title: Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1
Authors: Zhou, X. / Ren, W. / Bharath, S.R. / Tang, X. / He, Y. / Chen, C. / Liu, Z. / Li, D. / Song, H.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2473
Polymers49,7171
Non-polymers5302
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-4 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.090, 75.310, 111.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein / Pif1


Mass: 49716.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides sp. 2_1_16 (bacteria) / Gene: HMPREF0101_01022 / Production host: Escherichia coli (E. coli) / References: UniProt: D1JM21, UniProt: A0A7U8QDR9*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM MgCl2, 0.1 M Tris, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→62.4 Å / Num. obs: 33204 / % possible obs: 98.9 % / Redundancy: 7.5 % / Net I/σ(I): 20.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.15→44.78 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1598 5.13 %RANDOM
Rwork0.2109 ---
obs0.213 31136 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 32 135 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083533
X-RAY DIFFRACTIONf_angle_d0.9774790
X-RAY DIFFRACTIONf_dihedral_angle_d14.0232114
X-RAY DIFFRACTIONf_chiral_restr0.056542
X-RAY DIFFRACTIONf_plane_restr0.006608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.21940.30281370.27522624X-RAY DIFFRACTION99
2.2194-2.29870.34641290.26452639X-RAY DIFFRACTION99
2.2987-2.39080.31471450.2692646X-RAY DIFFRACTION99
2.3908-2.49960.29761410.26682665X-RAY DIFFRACTION99
2.4996-2.63140.32341300.2622637X-RAY DIFFRACTION99
2.6314-2.79620.35911570.26182685X-RAY DIFFRACTION99
2.7962-3.0120.31131440.25292681X-RAY DIFFRACTION100
3.012-3.31510.30711350.24552684X-RAY DIFFRACTION100
3.3151-3.79460.23451610.19552706X-RAY DIFFRACTION100
3.7946-4.77990.18871500.16642756X-RAY DIFFRACTION100
4.7799-44.78940.20111690.17232815X-RAY DIFFRACTION98

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