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Open data
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Basic information
Entry | Database: PDB / ID: 1bss | ||||||
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Title | ECORV-T93A/DNA/CA2+ | ||||||
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![]() | HYDROLASE/DNA / COMPLEX (ENDONUCLEASE ECORV-DNA) / 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 | ![]() | ||||||
![]() | Perona, J.J. / Horton, N.C. | ||||||
![]() | ![]() Title: Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases Authors: Horton, N.C. / Newberry, K.J. / Perona, J.J. #1: ![]() Title: Conformational Transitions and Structural Deformability of EcoRV Endonuclease Revealed by Crystallographic Analysis Authors: Perona, J.J. / Martin, A.M. #2: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1az0S S: Starting model for refinement |
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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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Components
#1: DNA chain | Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 28529.131 Da / Num. of mol.: 2 / Mutation: T93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04390, type II site-specific deoxyribonuclease #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 31018 / % possible obs: 75 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: PDB 1AZ0 Resolution: 2.15→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.15→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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