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- PDB-5crx: ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATIO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5crx | ||||||
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Title | ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE | ||||||
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![]() | PROTEIN/DNA / CRE RECOMBINASE / DNA BENDING / SITE SPECIFIC RECOMBINATION / PROTEIN-DNA INTERACTION / PROTEIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, F. / Gopaul, D.N. / Van Duyne, G.D. | ||||||
![]() | ![]() Title: Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse. Authors: Guo, F. / Gopaul, D.N. / Van Duyne, G.D. #1: ![]() Title: Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. Authors: Gopaul, D.N. / Guo, F. / Van Duyne, G.D. #2: ![]() Title: Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Authors: Guo, F. / Gopaul, D.N. / 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 | ![]() | 174.3 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.8 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4crxC ![]() 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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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 10759.968 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 38579.164 Da / Num. of mol.: 2 / Mutation: Y324F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: 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: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 5.6 / Method: vapor diffusion, hanging 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 / Detector: CCD / Date: Dec 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→99 Å / Num. obs: 32242 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 63.4 Å2 / Rsym value: 0.069 / Net I/σ(I): 12.59 |
Reflection shell | Resolution: 2.7→2.78 Å / Redundancy: 3.71 % / Mean I/σ(I) obs: 23.76 / Rsym value: 0.23 / % possible all: 93.9 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.23 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CRX Resolution: 2.7→48 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 50.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 48 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.437 / % reflection Rfree: 5 % / Rfactor Rwork: 0.337 |