+Open data
-Basic information
Entry | Database: PDB / ID: 1ixs | ||||||
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Title | Structure of RuvB complexed with RuvA domain III | ||||||
Components |
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Keywords | HYDROLASE / 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 | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Yamada, K. / Miyata, T. / Tsuchiya, D. / Oyama, T. / Fujiwara, Y. / Ohnishi, T. / Iwasaki, H. / Shinagawa, H. / Ariyoshi, M. / Mayanagi, K. / Morikawa, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ixs.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ixs.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ixs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ixs_validation.pdf.gz | 763.7 KB | Display | wwPDB validaton report |
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Full document | 1ixs_full_validation.pdf.gz | 784.7 KB | Display | |
Data in XML | 1ixs_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1ixs_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/1ixs ftp://data.pdbj.org/pub/pdb/validation_reports/ix/1ixs | HTTPS FTP |
-Related structure data
Related structure data | 1ixrC 1hqcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a heterodimer in the asymmetric unit. |
-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 71.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 13, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HQC Resolution: 3.2→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å
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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 |