+Open data
-Basic information
Entry | Database: PDB / ID: 5gki | ||||||||||||
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Title | Structure of EndoMS-dsDNA3 complex | ||||||||||||
Components |
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Keywords | HYDROLASE/DNA / ENDONUCLEASE / DNA COMPLEX / HYDROLASE-DNA complex | ||||||||||||
Function / homology | Function and homology information single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Thermococcus kodakarensis KOD1 (archaea) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Nakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Structure / Year: 2016 Title: Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease Authors: Nakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K.I. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gki.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gki.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gki ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gki | HTTPS FTP |
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-Related structure data
Related structure data | 5gkeC 5gkfC 5gkgC 5gkhC 5gkjC 5bsl C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28598.096 Da / Num. of mol.: 2 / Mutation: D165A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Strain: KOD1 / Gene: TK1898 / Production host: Escherichia coli (E. coli) References: UniProt: Q5JER9, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 4521.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4676.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 27 molecules
#4: Chemical | #5: Chemical | ChemComp-MPD / ( #6: 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: 3.91 Å3/Da / Density % sol: 68.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.16 M CALCIUM ACETATE, 80 MM SODIUM CACODYLATE, 14.4%(W/V) PEG8000, 20%(W/V) GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→24.72 Å / Num. obs: 23761 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4 % / Mean I/σ(I) obs: 9.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BSL 5bsl Resolution: 2.9→24.72 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→24.72 Å
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Refine LS restraints |
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LS refinement shell |
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