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Open data
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Basic information
Entry | Database: PDB / ID: 1in8 | ||||||
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Title | THERMOTOGA MARITIMA RUVB T158V | ||||||
![]() | HOLLIDAY JUNCTION DNA HELICASE RUVB | ||||||
![]() | DNA BINDING PROTEIN / AAA+-Class ATPase / Winged-Helix Domain / DNA translocase / Holliday Junction / Branch Migration Motor / Walker A / Walker B / Sensor 1 / Sensor 2 / Arginine Finger | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Putnam, C.D. / Clancy, S.B. / Tsuruta, H. / Wetmur, J.G. / Tainer, J.A. | ||||||
![]() | ![]() Title: Structure and mechanism of the RuvB Holliday junction branch migration motor. Authors: Putnam, C.D. / Clancy, S.B. / Tsuruta, H. / Gonzalez, S. / Wetmur, J.G. / Tainer, J.A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ACCORDING TO THE AUTHOR, THE BIOLOGICAL UNIT IS ACTUALLY A HEXAMER; HOWEVER, THE HEXAMER IS NOT REPRESENTED IN THE CRYSTAL PACKING. NON-CRYSTALLOGRAPHIC SYMMETRY OPERATIONS TO GENERATE THE HEXAMER ARE NOT AVAILABLE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.6 KB | Display | ![]() |
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Full document | ![]() | 792.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1in4SC ![]() 1in5C ![]() 1in6C ![]() 1in7C ![]() 1j7kC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37204.207 Da / Num. of mol.: 1 / Mutation: T158V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1M 1,6-hexanediol, 100 mM cobalt chloride, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
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: Sep 3, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 26948 / Num. obs: 26948 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 8.2 / Num. unique all: 2652 / % possible all: 97.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 87639 |
Reflection shell | *PLUS % possible obs: 97.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IN4 Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2174179.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.4 Å2 / ksol: 0.444 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.281 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.249 |