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Open data
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Basic information
Entry | Database: PDB / ID: 8zm6 | ||||||
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Title | Crystal structure of Thermolysin (Dose III) | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / thermolysin / radiation damage | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nam, K.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Thermolysin (Dose III) Authors: Nam, K.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.4 KB | Display | ![]() |
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PDB format | ![]() | 62.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 351 molecules ![](data/chem/img/ILE.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LYS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ILE / | ||
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#3: Chemical | ChemComp-LYS / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 74793 / % possible obs: 100 % / Redundancy: 32.6 % / CC1/2: 0.996 / Net I/σ(I): 32.89 |
Reflection shell | Resolution: 1.35→1.37 Å / Num. unique obs: 3665 / CC1/2: 0.703 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 12.733 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→34.18 Å
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Refine LS restraints |
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