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Yorodumi- PDB-1k0z: Crystal Structure of the PvuII endonuclease with Pr3+ and SO4 ion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0z | ||||||
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Title | Crystal Structure of the PvuII endonuclease with Pr3+ and SO4 ions bound in the active site at 2.05A. | ||||||
Components | Type II restriction enzyme PvuII | ||||||
Keywords | HYDROLASE / PvuII / endonuclease / restriction enzyme / catalysis / ions / xrays / lanthanades | ||||||
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: 2.05 Å | ||||||
Authors | Spyridaki, A. / Athanasiadis, A. / Matzen, C. / Lanio, T. / Jeltsch, A. / Simoncsits, A. / Scheuring-Vanamee, E. / Kokkinidis, M. / Pingoud, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k0z.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0z.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 1k0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0z ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0z | 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18239.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: PvuiiR / Plasmid: pPVU1 (pUC18 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P23657, type II site-specific deoxyribonuclease #2: Chemical | #3: Chemical | #4: 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: 2.88 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5 Details: Ammonium Sulfate, Ammonium Acetate, pH 5.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 23, 1995 / Details: monochromator |
Radiation | Monochromator: Si111/Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→21.43 Å / Num. all: 24251 / Num. obs: 24251 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 26.71 Å2 / Rsym value: 0.089 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1 / Num. unique all: 1894 / Rsym value: 0.657 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PVU Resolution: 2.05→21.43 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1549630.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.9366 Å2 / ksol: 0.315616 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→21.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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