+Open data
-Basic information
Entry | Database: PDB / ID: 1bgb | ||||||
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Title | ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / COMPLEX (ENDONUCLEASE-DNA) / 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 / DIFFERENCE FOURIER / Resolution: 2 Å | ||||||
Authors | Perona, J. / Horton, N.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. Authors: Horton, N.C. / Perona, J.J. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Role of Protein-Induced Bending in the Specificity of DNA Recognition-Crystal Structure of EcoRV Endonuclease Complexed with D(Aaagat) + D(Atctt) Authors: Horton, N.C. / Perona, J.J. #2: Journal: J.Mol.Biol. / Year: 1997 Title: Conformational Transitions and Structural Deformability of EcoRV Endonuclease Revealed by Crystallographic Analysis Authors: Perona, J.J. / Martin, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bgb.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bgb.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bgb ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bgb | 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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-Components
#1: DNA chain | Mass: 3334.186 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 28559.158 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALLIZED FROM 15% PEG 4K, 100 MM IMIDAZOLE, (PH 6.5), 150 MM NACL., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 25665 / % possible obs: 85 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.091 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.28 / % possible all: 71 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 27.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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