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- PDB-6fwr: Structure of DinG in complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 6fwr
TitleStructure of DinG in complex with ssDNA
Components
  • ATP-dependent DNA helicase DinG
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
KeywordsDNA BINDING PROTEIN / ATP / helicase / translocase
Function / homology
Function and homology information


DNA/RNA helicase activity / nucleobase-containing compound metabolic process / DNA duplex unwinding / SOS response / DNA helicase activity / 4 iron, 4 sulfur cluster binding / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity ...DNA/RNA helicase activity / nucleobase-containing compound metabolic process / DNA duplex unwinding / SOS response / DNA helicase activity / 4 iron, 4 sulfur cluster binding / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
ATP-dependent DNA helicase DinG / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 ...ATP-dependent DNA helicase DinG / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / ATP-dependent DNA helicase DinG / ATP-dependent DNA helicase DinG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCheng, K. / Wigley, D.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council and Cancer Research UKMR/N009258/1 United Kingdom
CitationJournal: Elife / Year: 2018
Title: DNA translocation mechanism of an XPD family helicase.
Authors: Cheng, K. / Wigley, D.B.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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

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Assembly

Deposited unit
A: ATP-dependent DNA helicase DinG
B: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2063
Polymers84,8542
Non-polymers3521
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-47 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.971, 133.867, 58.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ATP-dependent DNA helicase DinG


Mass: 81553.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dinG, CV83915_00780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4TNL0, UniProt: P27296*PLUS
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 3301.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.25 M KCl, 0.1M HEPES (pH 7.8) and 22% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.5→79.59 Å / Num. obs: 27857 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.54 Å / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→58.862 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.2457 1355 4.89 %
Rwork0.2108 --
obs0.2125 27688 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→58.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 216 8 118 5894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085912
X-RAY DIFFRACTIONf_angle_d1.1348063
X-RAY DIFFRACTIONf_dihedral_angle_d18.2753582
X-RAY DIFFRACTIONf_chiral_restr0.05912
X-RAY DIFFRACTIONf_plane_restr0.0061006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58950.38391540.29462531X-RAY DIFFRACTION98
2.5895-2.69310.2904940.27842634X-RAY DIFFRACTION99
2.6931-2.81570.30581210.25812595X-RAY DIFFRACTION100
2.8157-2.96410.31691220.24912613X-RAY DIFFRACTION100
2.9641-3.14980.29371400.24332586X-RAY DIFFRACTION100
3.1498-3.3930.29141320.21652637X-RAY DIFFRACTION100
3.393-3.73440.1981490.20152611X-RAY DIFFRACTION100
3.7344-4.27470.20061460.18632647X-RAY DIFFRACTION100
4.2747-5.38510.21321420.17242674X-RAY DIFFRACTION100
5.3851-58.87820.231550.19642805X-RAY DIFFRACTION100

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