+Open data
-Basic information
Entry | Database: PDB / ID: 1fok | ||||||
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Title | STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / COMPLEX (ENDONUCLEASE-DNA) / TYPE IIS / RESTRICTION ENDONUCLEASE / DEOXYRIBONUCLEASE / DNA HYDROLYSIS / DNA CLEAVAGE / 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 Similarity search - Function | ||||||
Biological species | Planomicrobium okeanokoites (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Aggarwal, D.A. / Wah, J.A. / Hirsch, L.F. / Dorner, I. / Schildkraut, A.K. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Structure of the multimodular endonuclease FokI bound to DNA. Authors: Wah, D.A. / Hirsch, J.A. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K. #1: Journal: FEBS Lett. / Year: 1997 Title: Crystallization and Preliminary X-Ray Analysis of Restriction Endonuclease Foki Bound to DNA Authors: Hirsch, J.A. / Wah, D.A. / Dorner, L.F. / Schildkraut, I. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fok.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fok.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1fok ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1fok | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6158.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / Strain: IFO12536 / Gene: FOKI / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 6108.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Protein | Mass: 65519.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planomicrobium okeanokoites (bacteria) / References: UniProt: P14870 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 62 % / Description: CRYSTALS WERE FLASH FROZEN IN NITROGEN STREAM. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop / Details: macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: F1 |
Detector | Type: SOL GRUNER, FUJI / Detector: CCD / Date: May 3, 1994 / Details: MIRRORS |
Radiation | Monochromator: BENT, TRIANGULAR SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 26253 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.325 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 100 Å / % possible obs: 98.5 % |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.8→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Rfactor Rfree error: 0.04 / 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 Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.354 |