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Open data
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Basic information
Entry | Database: PDB / ID: 6sck | ||||||
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Title | THERMOLYSIN IN COMPLEX WITH FRAGMENT J77 | ||||||
![]() | Thermolysin | ||||||
![]() | HYDROLASE / THERMOLYSIN / METALLOPROTEASE / FRAGMENT COMPLEX | ||||||
Function / homology | ![]() thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Magari, F. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J77 Authors: Magari, F. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.6 KB | Display | ![]() |
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PDB format | ![]() | 163.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694.1 KB | Display | ![]() |
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Full document | ![]() | 694.2 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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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 E
#1: Protein | Mass: 34360.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 6 types, 308 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/DAR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/DAR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-DAR / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO |
-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: Aug 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 63850 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 13.35 Å2 / CC1/2: 0.999 / Rsym value: 0.076 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.41→1.49 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 10112 / CC1/2: 0.94 / Rsym value: 0.497 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.41→46.39 Å / SU ML: 0.1064 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.6477
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→46.39 Å
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Refine LS restraints |
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LS refinement shell |
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