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Yorodumi- PDB-2hof: Crystal structure of the pre-cleavage synaptic complex in the cre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hof | ||||||
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Title | Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination | ||||||
Components |
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Keywords | recombination/DNA / CRE-LOXP PRECLEAVAGE SYNAPSE / recombination-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ghosh, K. / Van Duyne, G.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hof.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hof.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/2hof ftp://data.pdbj.org/pub/pdb/validation_reports/ho/2hof | HTTPS FTP |
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-Related structure data
Related structure data | 2hoiC 1crxS 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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-Components
#1: DNA chain | Mass: 10703.945 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 10815.003 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 38537.062 Da / Num. of mol.: 2 / Mutation: K201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: cre / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06956 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.36 % | ||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.078 Å |
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: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 46082 / Num. obs: 45638 / % possible obs: 99.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.05 / Χ2: 0.925 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.397 / Num. unique all: 2255 / Rsym value: 0.332 / Χ2: 0.873 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CRX Resolution: 2.4→29.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.968 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.258 / 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: 52.607 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.466 Å / Total num. of bins used: 20
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