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Open data
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Basic information
Entry | Database: PDB / ID: 1es8 | ||||||
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Title | Crystal structure of free BglII | ||||||
![]() | RESTRICTION ENDONUCLEASE BGLII | ||||||
![]() | HYDROLASE / RESTRICTION ENDONUCLEASE / RESTRICTION ENZYME / uncomplexed | ||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukacs, C.M. / Aggarwal, A.K. | ||||||
![]() | ![]() Title: Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease. Authors: Lukacs, C.M. / Kucera, R. / Schildkraut, I. / Aggarwal, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 39.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.7 KB | Display | ![]() |
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Full document | ![]() | 383.7 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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Components
#1: Protein | Mass: 26031.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q45488, type II site-specific deoxyribonuclease |
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#2: Chemical | ChemComp-ACY / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% isopropanol, 0.2 M sodium acetate, 0.1 M Bis-tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 Details: drop consists of equal amounts of protein and precipitant solutions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Mar 1, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→40 Å / Num. all: 10979 / Num. obs: 10979 / % possible obs: 99.4 % / Observed criterion σ(I): -2 / Redundancy: 3.1 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.4 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.152 / Num. unique all: 1083 / % possible all: 99.1 | ||||||||||||
Reflection | *PLUS Num. measured all: 33794 / Rmerge(I) obs: 0.057 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.138 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 10418 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.1 Å2 |