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- PDB-7f5i: X-ray structure of Clostridium perfringens-specific amidase endolysin -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f5i | ||||||
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Title | X-ray structure of Clostridium perfringens-specific amidase endolysin | ||||||
![]() | amidase | ||||||
![]() | HYDROLASE / endolysin / amidase | ||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kamitori, S. / Tamai, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+ -dependent amidase endolysin, Psa, catalytic domain. Authors: Sekiya, H. / Kamitori, S. / Nariya, H. / Matsunami, R. / Tamai, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 930.2 KB | Display | ![]() |
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Full document | ![]() | 930.3 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lbaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18967.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 13 / Type A / Gene: CPE1138 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM potassium bromide, 200 mM potassium thiocyanate, 0.1 M sodium acetate, 3 % w/v poly-gamma-glutamic acid, 5% w/v PEG 3350, pH 5.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→18.36 Å / Num. obs: 19657 / % possible obs: 99.7 % / Redundancy: 6.37 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2 / Num. unique obs: 1423 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LBA Resolution: 1.65→18.36 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.437 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.658 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→18.36 Å
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Refine LS restraints |
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