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- PDB-8yjc: Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yjc | ||||||
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Title | Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A | ||||||
![]() | Multifunctional autoprocessing repeat-in-toxin (MARTX) | ||||||
![]() | TOXIN / protease / Inositol hexaphosphate / activation | ||||||
Function / homology | INOSITOL HEXAKISPHOSPHATE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, L. / Khan, H. / Tan, L. / Li, X. / Zhang, G. / Im, Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of the activation of MARTX cysteine protease domain from Vibrio vulnificus. Authors: Chen, L. / Khan, H. / Tan, L. / Li, X. / Zhang, G. / Im, Y.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.7 KB | Display | ![]() |
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PDB format | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.8 KB | Display | ![]() |
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Full document | ![]() | 1016.5 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yjaC C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 24348.615 Da / Num. of mol.: 1 / Fragment: cysteine protease domain / Mutation: C3727A Source method: isolated from a genetically manipulated source Details: NCBI Reference Sequence: WP_058645630.1, MARTX cysteine protease domain, C3727A mutant. The N-terminal GSAMGS is a linker sequence to the cleavable His-tag by thrombin. Source: (gene. exp.) ![]() Details (production host): the N-terminal thrombin cleavable His-tag fusion Production host: ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-IHP / |
#4: Chemical | ChemComp-TRS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M HEPES pH 9.0, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 54914 / % possible obs: 97.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 12.96 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 46.8 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 2163 / % possible all: 76.4 |
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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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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→24.73 Å
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Refine LS restraints |
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LS refinement shell |
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