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Open data
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Basic information
Entry | Database: PDB / ID: 1ixr | ||||||
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Title | RuvA-RuvB complex | ||||||
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![]() | HYDROLASE / heterooligomeric complex / octameric RuvA / AAA-ATPase domain / complex with nucleotide | ||||||
Function / homology | ![]() Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.1 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721.1 KB | Display | ![]() |
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Full document | ![]() | 790 KB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is generated by the 222 crystallographic symmetry at the origin: (-x,-y,z), (x,-y,-z), and (-x,y,-z). |
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Components
#1: Protein | Mass: 20441.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 34801.312 Da / Num. of mol.: 1 / Fragment: residues 1-312 / Mutation: Y309R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ANP / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.82 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: NaCl, ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 24, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→44 Å / Num. all: 24710 / Num. obs: 24710 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.5 / % possible all: 97.6 |
Reflection | *PLUS Lowest resolution: 44 Å / Num. measured all: 139789 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.474 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.42 Å
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Refinement | *PLUS Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.268 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.393 / Rfactor Rwork: 0.371 |