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Open data
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Basic information
Entry | Database: PDB / ID: 5czw | ||||||||||||
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Title | Crystal structure of myroilysin | ||||||||||||
![]() | Myroilysin | ||||||||||||
![]() | HYDROLASE / propeptide / Inhibition / protease | ||||||||||||
Function / homology | Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / metalloendopeptidase activity / zinc ion binding / Myroilysin![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zhou, J. / Ran, T. / Xu, D. / Wang, W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Myroilysin is a New Bacterial Member of the M12A Family of Metzincin Metallopeptidases and Activated by a Cysteine-switch Mechanism Authors: Xu, D. / Zhou, J. / Lou, X. / He, J. / Ran, T. / Wang, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 26667.551 Da / Num. of mol.: 1 / Fragment: UNP residues 35-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris,PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 28643 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.69→1.69 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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: 19.363 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→20 Å
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Refine LS restraints |
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