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Open data
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Basic information
Entry | Database: PDB / ID: 5gkj | ||||||||||||
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Title | Structure of EndoMS in apo form | ||||||||||||
![]() | Endonuclease EndoMS | ||||||||||||
![]() | HYDROLASE / ENDONUCLEASE / DNA-BINDING | ||||||||||||
Function / homology | ![]() single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Nakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.4 KB | Display | ![]() |
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PDB format | ![]() | 76.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 456.5 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gkeC ![]() 5gkfC ![]() 5gkgC ![]() 5gkhC ![]() 5gkiC ![]() 5bsl C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28598.096 Da / Num. of mol.: 2 / Mutation: D165A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: KOD1 / Gene: TK1898 / Production host: ![]() ![]() References: UniProt: Q5JER9, Hydrolases; Acting on ester bonds |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.22 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→24.92 Å / Num. obs: 10762 / % possible obs: 97.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7 % / Mean I/σ(I) obs: 10.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BSL ![]() 5bsl Resolution: 3.2→24.11 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→24.11 Å
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Refine LS restraints |
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LS refinement shell |
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