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- PDB-2flc: Post-Reactive Complex of Restriction Endonuclease HinP1I with Nic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2flc | ||||||
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Title | Post-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium Ions | ||||||
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![]() | HYDROLASE/DNA / RESTRICTION ENDONUCLEASE / PROTEIN DIMERIZATON / DNA SUPERHELIX / PROTEIN-DNA-METAL ION COMPLEX / NICKED DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.9 KB | Display | ![]() |
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Full document | ![]() | 394.4 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fkcC ![]() 2fkhC ![]() 2fl3C ![]() 1ynmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 1175.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized Self-Annealing Oligonucleotide |
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#2: DNA chain | Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 28791.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: GenBank: 57116674, UniProt: Q5I6E6*PLUS, type II site-specific deoxyribonuclease |
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-Non-polymers , 3 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG1000, 400mM NaCl, 100mM Bis-Tris propane, and 5% ethylene glycol (5mM Magnesium Chloride was soaked into the crystal), pH 6.8, 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 17, 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: 2.59→34.1 Å / Num. all: 13460 / Num. obs: 13460 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.59→2.65 Å / Num. unique all: 1059 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1YNM Resolution: 2.59→34.1 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: 69.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.59→34.1 Å
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Refine LS restraints |
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