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- PDB-1b97: ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b97 | ||||||
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Title | ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP | ||||||
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![]() | HYDROLASE/DNA / ENDONUCLEASE / RESTRICTION / ECORV / 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 | ![]() ![]() ![]() | ||||||
![]() | Thomas, M.P. / Halford, S.E. / Brady, R.L. | ||||||
![]() | ![]() Title: Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group. Authors: Thomas, M.P. / Brady, R.L. / Halford, S.E. / Sessions, R.B. / Baldwin, G.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b94C ![]() 1b95C ![]() 1b96C ![]() 1rvaS S: Starting model for refinement C: citing same article ( |
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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: 28544.186 Da / Num. of mol.: 2 / Mutation: Q69L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P04390, type II site-specific deoxyribonuclease #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Oct 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 17144 / % possible obs: 92.7 % / Redundancy: 1.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.6 / % possible all: 87.5 |
Reflection | *PLUS Num. obs: 38240 / Num. measured all: 113353 |
Reflection shell | *PLUS % possible obs: 87.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RVA Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal target: 0.02 |