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Yorodumi- PDB-5u96: Crystal structure of the coiled-coil domain from Listeria Innocua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u96 | ||||||
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Title | Crystal structure of the coiled-coil domain from Listeria Innocua (Tetragonal Form) | ||||||
Components | Putative integrase | ||||||
Keywords | RECOMBINATION / site-specific recombination / coiled-coil | ||||||
Function / homology | Function and homology information DNA strand exchange activity / DNA integration / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Gupta, K. / Van Duyne, G.D. / Sharp, R. / Yuan, J.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Coiled-coil interactions mediate serine integrase directionality. Authors: Gupta, K. / Sharp, R. / Yuan, J.B. / Li, H. / Van Duyne, G.D. #1: Journal: Nucleic Acids Res. / Year: 2013 Title: Attachment site recognition and regulation of directionality by the serine integrases. Authors: Rutherford, K. / Yuan, P. / Perry, K. / Sharp, R. / 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 | 5u96.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u96.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 5u96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/5u96 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u96 | HTTPS FTP |
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-Related structure data
Related structure data | 5uaeC 5udoC 4kisS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 6074.780 Da / Num. of mol.: 8 / Fragment: Coiled-coil domain (UNP residues 350-400) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q928V6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M ammonium sulfate, 100 mM HEPES pH 7.5, and 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35.7 Å / Num. obs: 36018 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KIS Resolution: 1.95→35.688 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→35.688 Å
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Refine LS restraints |
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LS refinement shell |
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