+Open data
-Basic information
Entry | Database: PDB / ID: 2fok | ||||||
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Title | STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI | ||||||
Components | FOKI RESTRICTION ENDONUCLEASEFokI | ||||||
Keywords | NUCLEIC ACID RECOGNITION / DNA-BINDING PROTEIN / TYPE IIS RESTRICTION ENDONUCLEASE / DEOXYRIBONUCLEASE / DNA HYDROLYSIS / DNA CLEAVAGE / METALLOENZYME / METAL ION CATALYSIS | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Planomicrobium okeanokoites (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wah, D.A. / Bitinaite, J. / Schildkraut, I. / Aggarwal, A.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 1998 Title: Structure of FokI has implications for DNA cleavage. Authors: Wah, D.A. / Bitinaite, J. / Schildkraut, I. / Aggarwal, A.K. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: FokI Dimerization is Required for DNA Cleavage Authors: Bitinaite, J. / Wah, D.A. / Aggarwal, A.K. / Schildkraut, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fok.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fok.ent.gz | 190.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/2fok ftp://data.pdbj.org/pub/pdb/validation_reports/fo/2fok | HTTPS FTP |
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-Related structure data
Related structure data | 1fokS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 65833.625 Da / Num. of mol.: 2 / Fragment: FULL-LENGTH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / Strain: IFO12536 / Gene: FOKI / Production host: Escherichia coli (E. coli) References: UniProt: P14870, 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: 2.7 Å3/Da / Density % sol: 53.69 % Description: CRYSTALS WERE FLASH FROZEN IN NITROGEN STREAM. DATA WAS COLLECTED BY OSCILLATION. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN CRYSTALLIZED IN 22% PEG 8000, 0.4 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH 6.5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jan 20, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 61150 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.364 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FOK Resolution: 2.3→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING.
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Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.214 |