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Open data
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Basic information
Entry | Database: PDB / ID: 1esg | ||||||
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Title | RESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA. | ||||||
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![]() | HYDROLASE/DNA / Non-specific DNA-protein complex. / HYDROLASE-DNA COMPLEX | ||||||
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 | ![]() ![]() | ||||||
![]() | Viadiu, H. / Aggarwal, A.K. | ||||||
![]() | ![]() Title: Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Authors: Viadiu, H. / Aggarwal, A.K. #1: ![]() Title: A step towards understanding protein-DNA specificity: crystallization of the restriction endonuclease BamHI with a non-specific DNA Authors: Viadiu, H. / 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 | ![]() | 118.6 KB | Display | ![]() |
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PDB format | ![]() | 90.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 38.8 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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Unit cell |
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Details | A protein dimer with a double stranded DNA. |
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Components
#1: DNA chain | Mass: 2441.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphoramite synthesis | ||
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#2: DNA chain | Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphoramite synthesis | ||
#3: Protein | Mass: 24602.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23940, type II site-specific deoxyribonuclease #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.56 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 30% MPD, 10 mM sodium acetate (pH 4.8), 5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→10 Å / Num. all: 53008 / Num. obs: 53008 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.6 | ||||||||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.284 / Num. unique all: 5404 / % possible all: 85.2 | ||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 85.2 % |
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Processing
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Refinement | Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: protein: Engh & Huber, DNA: Parkinson et al.
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.1 Å2 |