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- PDB-1ixs: Structure of RuvB complexed with RuvA domain III -

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Basic information

Entry
Database: PDB / ID: 1ixs
TitleStructure of RuvB complexed with RuvA domain III
Components
  • Holliday junction DNA helicase ruvA
  • RuvB
KeywordsHYDROLASE / heterodimeric protein complex / AAA-ATPase domain / complex with nucleotide
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain ...Bacterial DNA recombination protein RuvA / DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvB, AAA lid domain / RuvA N terminal domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvA, C-terminal domain / RuvB AAA lid domain / Ubiquitin-associated (UBA) domain / RuvA domain 2-like / Helicase, Ruva Protein; domain 3 - #60 / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Holliday junction branch migration complex subunit RuvB / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
CitationJournal: Mol.Cell / Year: 2002
Title: Crystal Structure of the RuvA-RuvB Complex: A Structural Basis for the Holliday Junction Migrating Motor Machinery
Authors: Yamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K.
History
DepositionJul 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Holliday junction DNA helicase ruvA
B: RuvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6233
Polymers42,1172
Non-polymers5061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-12 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.060, 102.060, 137.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a heterodimer in the asymmetric unit.

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Components

#1: Protein Holliday junction DNA helicase ruvA


Mass: 6698.849 Da / Num. of mol.: 1 / Fragment: RuvA domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruva / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9F1Q3
#2: Protein RuvB


Mass: 35417.984 Da / Num. of mol.: 1 / Fragment: residues 1-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ruvb / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL87, EC: 3.6.1.3
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMRuvA domain III1drop
20.5 mMRuvB1drop
31 mMAMPPNP1drop
410 mMTris-HCl1droppH8.0
50.1 M1dropNaCl
610 %(w/v)glycerol1drop
710 mMTris-HCl1reservoirpH8.0
80.1 M1reservoirNaCl
910 %(w/v)glycerol1reservoir
1010 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 13, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 3.2→41 Å / Num. all: 235468 / Num. obs: 235468 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 41 Å / Num. obs: 12468 / Num. measured all: 235468 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.324

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQC

1hqc


Resolution: 3.2→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 633 -RANDOM
Rwork0.2313 ---
all-12434 --
obs-12434 99.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 31 0 2879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
X-RAY DIFFRACTIONc_angle_deg1.334
LS refinement shellResolution: 3.2→3.31 Å
RfactorNum. reflection% reflection
Rfree0.4718 59 -
Rwork0.35 --
obs-1209 94.3 %
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.4718 / Rfactor Rwork: 0.35

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