+Open data
-Basic information
Entry | Database: PDB / ID: 2b0d | ||||||
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Title | EcoRV Restriction Endonuclease/GAATTC/Ca2+ | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein-nucleic acid recognition / indirect readout / restriction enzyme / substrate specificity / noncognate / 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Hiller, D.A. / Rodriguez, A.M. / Perona, J.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC Authors: Hiller, D.A. / Rodriguez, A.M. / Perona, J.J. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease Authors: Martin, A.M. / Sam, M.D. / Reich, N.O. / Perona, J.J. #2: Journal: Biochemistry / Year: 2003 Title: Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence Authors: Hiller, D.A. / Fogg, J.M. / Martin, A.M. / Beechem, J.M. / Reich, N.O. / Perona, J.J. #3: Journal: Biochemistry / Year: 2004 Title: DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites Authors: Horton, N.C. / 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 | 2b0d.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b0d.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/2b0d ftp://data.pdbj.org/pub/pdb/validation_reports/b0/2b0d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3356.235 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) / Gene: ecoRVR / Plasmid: pBSRV / Production host: Escherichia coli (E. coli) / Strain (production host): mm294 References: UniProt: P04390, type II site-specific deoxyribonuclease #3: Chemical | #4: 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: 39.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4K, Hepes, NaCl, CaCl2, Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 297K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 30291 / % possible obs: 89.1 % / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→2.1 Å / Mean I/σ(I) obs: 3.1 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→6 Å /
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Displacement parameters | Biso mean: 19.952 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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