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Yorodumi- PDB-1b96: ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b96 | ||||||
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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 | ||||||
Components |
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Keywords | HYDROLASE/DNA / ENDONUCLEASE / RESTRICTION / ECORV / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Thomas, M.P. / Halford, S.E. / Brady, R.L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b96.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b96.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b96 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b96 | HTTPS FTP |
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-Related structure data
Related structure data | 1b94C 1b95C 1b97C 1rvaS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 28560.143 Da / Num. of mol.: 2 / Mutation: Q69E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Gene: ECORVR / Plasmid: PBSKRV / 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: 2.05 Å3/Da / Density % sol: 40.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→12.5 Å / Num. obs: 21703 / % possible obs: 96.5 % / Redundancy: 1.56 % / Biso Wilson estimate: 29.18 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.61 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.6 / % possible all: 94.8 |
Reflection | *PLUS Num. measured all: 148523 |
Reflection shell | *PLUS % possible obs: 94.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RVA Resolution: 2.3→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→12.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal target: 0.02 |