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- PDB-5fhe: Crystal structure of Bacteroides Pif1 bound to ssDNA -

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Basic information

Entry
Database: PDB / ID: 5fhe
TitleCrystal structure of Bacteroides Pif1 bound to ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Uncharacterized protein
KeywordsHYDROLASE/DNA / Pif1 helicase / DNA helicase / HYDROLASE-DNA complex
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 / DNA / UvrD_C_2 domain-containing protein / UvrD_C_2 domain-containing protein
Similarity search - Component
Biological speciesBacteroides sp. 2_1_16 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 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 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2685
Polymers52,7142
Non-polymers5543
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-35 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.442, 87.442, 149.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 4 M sodium formate, 0.1 M HEPES, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→33.8 Å / Num. obs: 15236 / % possible obs: 99.9 % / Redundancy: 9.4 % / Net I/σ(I): 14.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.9→33.792 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 818 5.38 %RANDOM
Rwork0.2226 ---
obs0.2255 15209 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→33.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 120 33 0 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093558
X-RAY DIFFRACTIONf_angle_d1.1544855
X-RAY DIFFRACTIONf_dihedral_angle_d17.5882088
X-RAY DIFFRACTIONf_chiral_restr0.059564
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.08180.42261200.36472364X-RAY DIFFRACTION100
3.0818-3.31960.37561370.33642349X-RAY DIFFRACTION100
3.3196-3.65330.35751480.26882352X-RAY DIFFRACTION100
3.6533-4.18110.29881240.22492402X-RAY DIFFRACTION100
4.1811-5.26450.21261580.18252382X-RAY DIFFRACTION100
5.2645-33.79450.25391310.19032542X-RAY DIFFRACTION100
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)
10.0634-0.67960.00860.8133-0.29270.15650.35070.2598-0.13270.5232-0.40190.64280.1139-0.89840.41930.5563-0.19210.08150.98740.0810.9685-30.250855.846570.5026
22.7968-0.5822-0.41030.5464-0.62222.87180.20210.10040.0515-0.2558-0.19840.14680.1426-0.09210.00030.6915-0.1411-0.03070.52170.04130.553-15.298255.760858.7964
30.3883-1.09910.09780.57870.2950.2352-0.19770.06110.43840.38720.20160.2071-1.2053-0.210.00010.98230.05580.07920.7709-0.0040.9039-21.684670.993582.5842
40.386-0.4910.51910.35310.07430.2673-0.0847-0.0877-0.37280.4685-0.3325-0.8819-0.49960.9282-0.00130.9286-0.16930.08390.78290.07860.6739-3.46657.716589.5525
50.656-0.77771.21442.3579-0.52290.84550.1203-0.18140.183-0.24050.05320.04430.43340.24780.00050.7405-0.1806-0.01220.75950.01640.5703-0.149840.608279.5
6-0.00040.6272-0.2391-0.021-0.14610.05470.3354-0.35460.5797-0.7093-0.33280.31810.31240.4823-0.02781.18910.15560.12370.74660.18480.77210.592139.776163.6761
70.02151.1980.16752.06880.22792.4118-0.0398-0.05540.22080.5455-0.16070.2423-0.40460.04290.00030.5666-0.09190.06770.495-0.00490.6335-13.406565.137478.062
8-0.14810.09770.1030.0191-0.06340.36210.03090.54250.2387-1.315-0.82530.2645-0.53620.1877-0.00050.8724-0.10070.00450.9764-0.02040.8043-3.747854.262867.5667
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 246 )
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 349 )
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 432 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 8 )

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