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Yorodumi- PDB-1ni0: Structure of the Y94F mutant of the restriction endonuclease PvuII -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ni0 | ||||||
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Title | Structure of the Y94F mutant of the restriction endonuclease PvuII | ||||||
Components | Type II restriction enzyme PvuII | ||||||
Keywords | HYDROLASE / Restriction endonuclease / PvuII / Point mutation | ||||||
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 | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Tucker, P.A. / Kokkinidis, M. / Nicolaki, S. / Kotsifaki, D. | ||||||
Citation | Journal: To be Published Title: Structure of the Y94F mutant of the restriction endonuclease PvuII Authors: Tucker, P.A. / Kokkinidis, M. / Nicolaki, S. / Kotsifaki, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ni0.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ni0.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ni0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1ni0 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1ni0 | HTTPS FTP |
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-Related structure data
Related structure data | 1pvuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18497.148 Da / Num. of mol.: 3 / Mutation: Y94F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: PVUIIR / Plasmid: N-A / Production host: Escherichia coli (E. coli) References: UniProt: P23657, type II site-specific deoxyribonuclease #2: 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: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: N/A, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 4, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.801 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 26081 / Num. obs: 25788 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 11 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1267 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PVU Resolution: 2.5→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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