+Open data
-Basic information
Entry | Database: PDB / ID: 3c28 | ||||||
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Title | Crystal structure of the product synapse complex | ||||||
Components |
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Keywords | recombination/DNA / Synaptic complex / DNA integration / DNA recombination / recombination-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteriophage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Ghosh, K. / Van Duyne, G.D. | ||||||
Citation | Journal: To be Published Title: Detailed study on Synapsis in Cre-loxP recombination reaction Authors: Ghosh, K. / 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 | 3c28.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c28.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/3c28 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c28 | HTTPS FTP |
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-Related structure data
Related structure data | 1crxS S: Starting model for refinement |
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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: 10470.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: LoxP DNA from Phage P1 | ||
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#2: DNA chain | Mass: 10439.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: LoxP DNA from Phage P1 | ||
#3: Protein | Mass: 36405.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage P1 (virus) / Gene: cre / 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: 3.16 Å3/Da / Density % sol: 61.13 % | ||||||||||||||||||||||||||||
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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: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2002 / Details: Monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 41399 / Num. obs: 41399 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 1 % / Rmerge(I) obs: 0.073 / Χ2: 1.221 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.57 Å / Rmerge(I) obs: 0.323 / Num. unique all: 3363 / Χ2: 0.602 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Starting model: 1CRX Resolution: 2.6→40.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.842 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.521 / ESU R Free: 0.336 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→40.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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