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- PDB-5fhg: Structure of unliganded Pif1 from Bacteroides sp -

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Basic information

Entry
Database: PDB / ID: 5fhg
TitleStructure of unliganded Pif1 from Bacteroides sp
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
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 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
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)99,4342
Polymers99,4342
Non-polymers00
Water14,106783
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)49,7171
Polymers49,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)49,7171
Polymers49,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.485, 123.485, 66.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Uncharacterized protein / Pif1


Mass: 49716.941 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
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: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→61.7 Å / Num. obs: 61720 / % possible obs: 91.3 % / Redundancy: 3.2 % / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2→58.534 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3017 4.89 %RANDOM
Rwork0.19 ---
obs0.1931 61694 90.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→58.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5849 0 0 788 6637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076041
X-RAY DIFFRACTIONf_angle_d0.8198173
X-RAY DIFFRACTIONf_dihedral_angle_d11.3323623
X-RAY DIFFRACTIONf_chiral_restr0.057932
X-RAY DIFFRACTIONf_plane_restr0.0051033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03130.3211450.2382572X-RAY DIFFRACTION88
2.0313-2.06460.30161590.23522527X-RAY DIFFRACTION89
2.0646-2.10020.28911390.22232520X-RAY DIFFRACTION87
2.1002-2.13840.25141090.21712578X-RAY DIFFRACTION87
2.1384-2.17950.25971230.21092505X-RAY DIFFRACTION87
2.1795-2.2240.30331240.20442552X-RAY DIFFRACTION86
2.224-2.27240.27941420.21822501X-RAY DIFFRACTION86
2.2724-2.32520.29041190.20642544X-RAY DIFFRACTION86
2.3252-2.38340.30321410.19572534X-RAY DIFFRACTION87
2.3834-2.44780.27131310.20192534X-RAY DIFFRACTION87
2.4478-2.51990.25391260.18822599X-RAY DIFFRACTION89
2.5199-2.60120.26491510.19492572X-RAY DIFFRACTION89
2.6012-2.69420.26471290.1952686X-RAY DIFFRACTION91
2.6942-2.8020.28211400.19532685X-RAY DIFFRACTION92
2.802-2.92950.3051070.2012718X-RAY DIFFRACTION92
2.9295-3.0840.25121330.19612726X-RAY DIFFRACTION93
3.084-3.27720.25551550.19222729X-RAY DIFFRACTION93
3.2772-3.53020.24421230.16952824X-RAY DIFFRACTION96
3.5302-3.88540.22261520.16182896X-RAY DIFFRACTION98
3.8854-4.44740.19481490.15332887X-RAY DIFFRACTION98
4.4474-5.60260.2161400.16332991X-RAY DIFFRACTION100
5.6026-58.55910.25431800.22312997X-RAY DIFFRACTION99

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