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- PDB-1eo4: ECORV BOUND TO MN2+ AND COGNATE DNA CONTAINING A 3'S SUBSTITION A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1eo4 | |||||||||
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Title | ECORV BOUND TO MN2+ AND COGNATE DNA CONTAINING A 3'S SUBSTITION AT THE CLEAVAGE SITE | |||||||||
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![]() | hydrolase/DNA / Protein-DNA complex / restriction endonuclease / DNA analog / hydrolase-DNA COMPLEX | |||||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Horton, N.C. / Connolly, B.A. / Perona, J.J. | |||||||||
![]() | Journal: J.Am.Chem.Soc. / Year: 2000 Title: Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study Authors: Horton, N.C. / Connolly, B.A. / Perona, J.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.7 KB | Display | ![]() |
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PDB format | ![]() | 94.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 407.9 KB | Display | ![]() |
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Full document | ![]() | 414.3 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 | The biological assembly is a dimer composed of chains A and B / The biological assembly is a duplex composed of chains C and D |
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Components
#1: DNA chain | Mass: 3348.276 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 28690.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04390, type II site-specific deoxyribonuclease #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 4000, 0.1M HEPES, 0.15M NaCl, 50 mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 36838 / Num. obs: 36838 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 1.96 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.362 / Num. unique all: 4101 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 72080 |
Reflection shell | *PLUS % possible obs: 95 % / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Resolution: 1.9→4.9 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: X-Plor
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Refinement step | Cycle: LAST / Resolution: 1.9→4.9 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 2.1 % / Rfactor obs: 0.213 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.7 Å2 |