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Yorodumi- PDB-1eo3: INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eo3 | |||||||||
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Title | INHIBITION OF ECORV ENDONUCLEASE BY DEOXYRIBO-3'-S-PHOSPHOROTHIOLATES: A HIGH RESOLUTION X-RAY CRYSTALLOGRAPHIC STUDY | |||||||||
Components |
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Keywords | hydrolase/DNA / Protein-DNA complex / restriction endonuclease / DNA analog / hydrolase-DNA COMPLEX | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Horton, N.C. / Connolly, B.A. / Perona, J.J. | |||||||||
Citation | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eo3.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eo3.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/1eo3 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/1eo3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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 strands C and D |
-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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P04390, type II site-specific deoxyribonuclease #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.66 % | ||||||||||||||||||||||||||||||||||||||||||
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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 MgCl2, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 31662 / Num. obs: 31662 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 1.77 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.358 / Num. unique all: 4498 / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 55892 |
Reflection shell | *PLUS % possible obs: 90.5 % / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 2→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: 2→4.9 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 4.9 Å / σ(F): 2 / % reflection Rfree: 6 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.29 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.2 Å2 |