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- PDB-2fkc: Crystal Form I of Pre-Reactive Complex of Restriction Endonucleas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fkc | ||||||
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Title | Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ion | ||||||
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![]() | HYDROLASE/DNA / RESTRICTION ENDONUCLEASE / PROTEIN DIMERIZATON / DNA SUPERHELIX / PROTEIN-DNA-METAL ION COMPLEX / 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 | ![]() | 135.8 KB | Display | ![]() |
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PDB format | ![]() | 102.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.8 KB | Display | ![]() |
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Full document | ![]() | 403.6 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fkhC ![]() 2fl3C ![]() 2flcC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized Self-Annealing Oligonucleotide #2: Protein | Mass: 28791.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: GenBank: 57116674, UniProt: Q5I6E6*PLUS, type II site-specific deoxyribonuclease #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 7.5%(v/v) ethanol, 1.5M NaCl, 100mM Bis-Tris propane pH 7.8, and 20mM CaCl2, 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: Feb 27, 2005 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97179 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→19.89 Å / Num. all: 31659 / Num. obs: 31659 / % possible obs: 94.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.368 / Num. unique all: 3183 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1YNM Resolution: 2.39→19.89 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: 59 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.39→19.89 Å
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Refine LS restraints |
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