+
Open data
-
Basic information
Entry | Database: PDB / ID: 1in6 | ||||||
---|---|---|---|---|---|---|---|
Title | THERMOTOGA MARITIMA RUVB K64R MUTANT | ||||||
![]() | HOLLIDAY JUNCTION DNA HELICASE RUVB | ||||||
![]() | DNA BINDING PROTEIN / AAA+-Class ATPase / Winged-Helix Domain / Holliday Junction / Branch Migration / 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 |
| ||||||
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. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 812.6 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1in4SC ![]() 1in5C ![]() 1in7C ![]() 1in8C ![]() 1j7kC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37234.191 Da / Num. of mol.: 1 / Mutation: K64R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2000 |
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: 1.8→20 Å / Num. all: 29025 / Num. obs: 29025 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2569 / % possible all: 79.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 77808 |
Reflection shell | *PLUS % possible obs: 79.8 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IN4 Resolution: 1.8→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3157157.7 / 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.73 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.322 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.307 |