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- PDB-1c7y: E.COLI RUVA-HOLLIDAY JUNCTION COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1c7y
TitleE.COLI RUVA-HOLLIDAY JUNCTION COMPLEX
Components
  • DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
  • DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
  • DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
  • DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
  • DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
  • DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
  • DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
  • DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
  • HOLLIDAY JUNCTION DNA HELICASE RUVA
KeywordsRECOMBINATION/DNA / helix-hairpin-helix / protein-DNA complex / homologous recombination / Holliday junction / RECOMBINATION-DNA COMPLEX
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / recombinational repair / SOS response / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 ...Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsAriyoshi, M. / Nishino, T. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer.
Authors: Ariyoshi, M. / Nishino, T. / Iwasaki, H. / Shinagawa, H. / Morikawa, K.
History
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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
B: DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
C: DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
E: DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
F: DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
G: DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
H: DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
I: DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA


Theoretical massNumber of molelcules
Total (without water)52,6459
Polymers52,6459
Non-polymers00
Water0
1
B: DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
C: DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
E: DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
F: DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
G: DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
H: DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
I: DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA

B: DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
C: DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
E: DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
F: DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
G: DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
H: DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
I: DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA

B: DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
C: DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
E: DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
F: DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
G: DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
H: DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
I: DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA

B: DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')
C: DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')
D: DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')
E: DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')
F: DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')
G: DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')
H: DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')
I: DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')
A: HOLLIDAY JUNCTION DNA HELICASE RUVA


Theoretical massNumber of molelcules
Total (without water)210,57936
Polymers210,57936
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Unit cell
Length a, b, c (Å)158.65, 158.65, 158.65
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number211
Cell settingcubic
Space group name H-MI432

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Components

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DNA chain , 8 types, 8 molecules BCDEFGHI

#1: DNA chain DNA (5'-D(P*DAP*DAP*DGP*DTP*DTP*DGP*DGP*DGP*DAP*DTP*DTP*DGP*DT)-3')


Mass: 4061.655 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*DCP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DAP*DAP*DGP*DC)-3')


Mass: 3693.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*DGP*DCP*DTP*DTP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DGP*DA)-3')


Mass: 3944.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DGP*DAP*DA)-3')


Mass: 3782.476 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(P*DTP*DTP*DCP*DAP*DCP*DCP*DCP*DTP*DAP*DAP*DCP*DCP*DA)-3')


Mass: 3855.539 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: DNA chain DNA (5'-D(P*DGP*DAP*DCP*DAP*DCP*DAP*DCP*DAP*DTP*DTP*DCP*DG)-3')


Mass: 3631.394 Da / Num. of mol.: 1 / Source method: obtained synthetically
#7: DNA chain DNA (5'-D(P*DCP*DGP*DAP*DAP*DTP*DGP*DTP*DGP*DTP*DGP*DTP*DCP*DT)-3')


Mass: 3997.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
#8: DNA chain DNA (5'-D(P*DCP*DAP*DAP*DTP*DCP*DCP*DCP*DAP*DAP*DCP*DTP*DT)-3')


Mass: 3566.357 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#9: Protein HOLLIDAY JUNCTION DNA HELICASE RUVA


Mass: 22111.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P0A809

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, sodium chloride, glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2glycerol11
3NaClSodium chloride11
4(NH4)2SO411
5glycerol12
6NaClSodium chloride12
7(NH4)2SO412
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMes/NaOH1reservoir
22.0-2.2 Mammonium sulfate1reservoir
35 %glycerol1reservoir
41
51
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→80 Å / Num. all: 7136 / Num. obs: 7136 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 47
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.275 / Num. unique all: 691 / % possible all: 100
Reflection
*PLUS
Num. measured all: 143269
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.9refinement
RefinementResolution: 3.1→45.8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 3475770.71 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 631 9.7 %random
Rwork0.249 ---
obs0.25 6491 99.9 %-
all-6491 --
Solvent computationBsol: 88.2948 Å2 / ksol: 0.425315 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-6 Å
Luzzati sigma a0.36 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 2038 0 0 3565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shellResolution: 3.1→3.24 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.365 86 10.9 %
Rwork0.337 705 -
obs--100 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21

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