+Open data
-Basic information
Entry | Database: PDB / ID: 1es8 | ||||||
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Title | Crystal structure of free BglII | ||||||
Components | RESTRICTION ENDONUCLEASE BGLII | ||||||
Keywords | HYDROLASE / RESTRICTION ENDONUCLEASE / RESTRICTION ENZYME / uncomplexed | ||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Lukacs, C.M. / Aggarwal, A.K. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1es8.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1es8.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1es8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es8 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: Protein | Mass: 26031.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793, 0.9789, 0.9689 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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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 |