+Open data
-Basic information
Entry | Database: PDB / ID: 3ebc | ||||||
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Title | Structure of N141A HincII with Cognate DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / intermediate / mutant / dimerization / R-loop / Endonuclease / Hydrolase / Nuclease / Restriction system / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||
Authors | Little, E.J. / Babic, A.C. / Horton, N.C. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Early Interrogation and Recognition of DNA Sequence by Indirect Readout Authors: Little, E.J. / Babic, A.C. / Horton, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ebc.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebc.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ebc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebc ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36593.496 Da / Num. of mol.: 2 / Mutation: N141A Source method: isolated from a genetically manipulated source Details: N-terminal hexaHis Tag / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Plasmid: pET Blue2 / Production host: Escherichia coli (E. coli) References: UniProt: P17743, type II site-specific deoxyribonuclease #2: DNA chain | | Mass: 4322.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HincII Cognate CG #3: DNA chain | | Mass: 4242.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HincII Cognate CG #4: Chemical | ChemComp-MN / | #5: 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 grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG 4000, 0.1M imidazole buffer, 0.2M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K | ||||||||||||||||||||||||||||
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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: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2007 / Details: mirrors |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→43.56 Å / Num. all: 18533 / Num. obs: 17810 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 1.9 |
Reflection shell | Highest resolution: 2.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.9 / Num. unique all: 18532 / % possible all: 96.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→43.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.873 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.803 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.9 / ESU R Free: 0.383 / 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 max: 99.83 Å2 / Biso mean: 27.531 Å2 / Biso min: 6.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→43.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.547→2.613 Å / Total num. of bins used: 20
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