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- PDB-8byk: The structure of MadC from Clostridium maddingley reveals new ins... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8byk | |||||||||
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Title | The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases | |||||||||
![]() | Lanthionine synthetase C-like protein | |||||||||
![]() | BIOSYNTHETIC PROTEIN / cyclase / lantibiotic / biosynthetic | |||||||||
Function / homology | Subtilin biosynthesis protein SpaC / Type I lantibiotic biosynthesis cyclase / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Lanthionine synthetase C-like protein / ACETATE ION / Lanthionine synthetase C-like protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Knospe, C.V. / Kamel, M. / Spitz, O. / Hoeppner, A. / Galle, S. / Reiners, J. / Kedrov, A. / Smits, S.H. / Schmitt, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases. Authors: Knospe, C.V. / Kamel, M. / Spitz, O. / Hoeppner, A. / Galle, S. / Reiners, J. / Kedrov, A. / Smits, S.H.J. / Schmitt, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.6 KB | Display | ![]() |
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PDB format | ![]() | 161.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50820.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 302 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-CL / | #7: 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: 2.07 Å3/Da / Density % sol: 40.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: lithium chloride and MPD |
-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 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.89 Å / Num. obs: 47068 / % possible obs: 99.97 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 29.63 |
Reflection shell | Resolution: 1.7→1.761 Å / Num. unique obs: 4591 / CC1/2: 0.995 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 24.47 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→41.89 Å
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Refine LS restraints |
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