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- PDB-2hoi: Crystal structure of the tetrameric pre-cleavage synaptic complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hoi | ||||||
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Title | Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination | ||||||
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![]() | RECOMBINATION/DNA / CRE-LOXP PRECLEAVAGE SYNAPSE / RECOMBINATION-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghosh, K. / Van Duyne, G.D. | ||||||
![]() | ![]() Title: Synapsis of loxP sites by Cre recombinase. Authors: Ghosh, K. / Guo, F. / Van Duyne, G.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 350.5 KB | Display | ![]() |
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PDB format | ![]() | 274.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2hofC ![]() 1crxS 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: DNA chain | Mass: 10703.945 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 10815.003 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 38537.062 Da / Num. of mol.: 4 / Mutation: K201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.56 % | ||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: MPD, SODIUM ACETATE, CALCIUM CHLORIDE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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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: Mar 5, 2003 / Details: MONOCHROMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.601→19.92 Å / Num. all: 72945 / Num. obs: 59441 / % possible obs: 81.49 % / Rsym value: 0.09 |
Reflection shell | Highest resolution: 2.601 Å / Rsym value: 0.198 / % possible all: 81.64 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1CRX Resolution: 2.601→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.873 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.791 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.818 Å2
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Refinement step | Cycle: LAST / Resolution: 2.601→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.601→2.667 Å / Total num. of bins used: 20
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