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Yorodumi- PDB-1b95: ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b95 | ||||||
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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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1b95.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b95.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b95_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 1b95_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 1b95_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 1b95_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b95 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b95 | HTTPS FTP |
-Related structure data
Related structure data | 1b94C 1b96C 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: 28559.158 Da / Num. of mol.: 2 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.5418 |
Detector | Date: Mar 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: 2.05→30 Å / Num. obs: 29870 / % possible obs: 95.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2.05→2.21 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 9.8 / % possible all: 86.6 |
Reflection | *PLUS Num. measured all: 73981 |
Reflection shell | *PLUS % possible obs: 86.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RVA Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal target: 0.02 |