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Yorodumi- PDB-2fl3: Binary Complex of Restriction Endonuclease HinP1I with Cognate DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fl3 | ||||||
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Title | Binary Complex of Restriction Endonuclease HinP1I with Cognate DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / RESTRICTION ENDONUCLEASE / PROTEIN DIMERIZATON / DNA SUPERHELIX / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Horton, J.R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2006 Title: DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Authors: Horton, J.R. / Zhang, X. / Maunus, R. / Yang, Z. / Wilson, G.G. / Roberts, R.J. / Cheng, X. #1: Journal: Nucleic Acids Res. / Year: 2005 Title: Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI Authors: Yang, Z. / Horton, J.R. / Maunus, R. / Wilson, G.G. / Roberts, R.J. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fl3.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fl3.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/2fl3 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/2fl3 | HTTPS FTP |
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-Related structure data
Related structure data | 2fkcC 2fkhC 2flcC 1ynmS 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: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized Self-Annealing Oligonucleotide #2: Protein | | Mass: 28791.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hinP1IR / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): PR1 References: GenBank: 57116674, UniProt: Q5I6E6*PLUS, type II site-specific deoxyribonuclease #3: 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: 2.91 Å3/Da / Density % sol: 57.72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 20% PEG1000, 400mM NaCl, 100mM Bis-Tris propane, and 5% ethylene glycol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2005 |
Radiation | Monochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→34.17 Å / Num. all: 15524 / Num. obs: 15524 / % possible obs: 89 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 20.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.39→2.48 Å / Num. unique all: 854 / % possible all: 50.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1YNM Resolution: 2.39→34.17 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 68.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.39→34.17 Å
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Refine LS restraints |
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