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- PDB-6fws: Structure of DinG in complex with ssDNA and ADPBeF -

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Basic information

Entry
Database: PDB / ID: 6fws
TitleStructure of DinG in complex with ssDNA and ADPBeF
Components
  • ATP-dependent DNA helicase DinG
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
KeywordsDNA BINDING PROTEIN / ATP / helicase / translocase / DNA binding
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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCheng, K. / Wigley, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,14312
Polymers169,4054
Non-polymers1,7388
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-98 kcal/mol
Surface area60470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.771, 119.751, 126.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-dependent DNA helicase DinG


Mass: 81553.234 Da / Num. of mol.: 2
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

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DNA chain , 2 types, 2 molecules CD

#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: DNA chain DNA (5'-D(*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)

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Non-polymers , 5 types, 369 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MgCl2, 0.1M HEPES (pH 7.0), and 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.5→63.37 Å / Num. obs: 58152 / % possible obs: 99.5 % / Redundancy: 4.6 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→63.37 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2557 2806 4.85 %
Rwork0.2192 --
obs0.221 57827 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→63.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10894 412 80 361 11747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811652
X-RAY DIFFRACTIONf_angle_d1.0815889
X-RAY DIFFRACTIONf_dihedral_angle_d19.4047045
X-RAY DIFFRACTIONf_chiral_restr0.0641798
X-RAY DIFFRACTIONf_plane_restr0.0061972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54320.37961330.32972671X-RAY DIFFRACTION97
2.5432-2.58950.36161250.3142682X-RAY DIFFRACTION98
2.5895-2.63930.34651600.30142669X-RAY DIFFRACTION98
2.6393-2.69310.34411320.28762700X-RAY DIFFRACTION99
2.6931-2.75170.37651260.28262739X-RAY DIFFRACTION98
2.7517-2.81570.3241540.27222683X-RAY DIFFRACTION98
2.8157-2.88610.36161400.26322711X-RAY DIFFRACTION99
2.8861-2.96420.30651190.2582739X-RAY DIFFRACTION99
2.9642-3.05140.32631170.25242768X-RAY DIFFRACTION99
3.0514-3.14990.29611280.24532730X-RAY DIFFRACTION99
3.1499-3.26240.2931290.24762733X-RAY DIFFRACTION99
3.2624-3.39310.26371290.2242760X-RAY DIFFRACTION100
3.3931-3.54750.24131350.20072772X-RAY DIFFRACTION99
3.5475-3.73450.19281360.19472769X-RAY DIFFRACTION100
3.7345-3.96840.21951450.19252775X-RAY DIFFRACTION100
3.9684-4.27480.21721640.18462744X-RAY DIFFRACTION100
4.2748-4.70480.20241580.17352782X-RAY DIFFRACTION100
4.7048-5.38530.20911940.17322757X-RAY DIFFRACTION100
5.3853-6.78370.23061400.21912854X-RAY DIFFRACTION100
6.7837-63.39030.23251420.18652983X-RAY DIFFRACTION100

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