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Yorodumi- PDB-8yja: Structure of Vibrio vulnificus MARTX cysteine protease domain lac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yja | ||||||
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Title | Structure of Vibrio vulnificus MARTX cysteine protease domain lacking beta-flap | ||||||
Components | MARTX cysteine protease domain | ||||||
Keywords | TOXIN / protease / Inositol hexaphosphate / activation | ||||||
Function / homology | INOSITOL HEXAKISPHOSPHATE Function and homology information | ||||||
Biological species | Vibrio vulnificus MO6-24/O (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chen, L. / Khan, H. / Tan, L. / Li, X. / Zhang, G. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plos One / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yja.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yja.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 8yja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yja_validation.pdf.gz | 973.9 KB | Display | wwPDB validaton report |
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Full document | 8yja_full_validation.pdf.gz | 975.6 KB | Display | |
Data in XML | 8yja_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 8yja_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/8yja ftp://data.pdbj.org/pub/pdb/validation_reports/yj/8yja | HTTPS FTP |
-Related structure data
Related structure data | 8yjcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22678.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI Reference Sequence: WP_058645630.1. A fragment of MARTX cysteine protease domain lacking the C-terminal beta-flap. The N-terminal GSAMGS is a linker sequence from the plasmid vector for ...Details: NCBI Reference Sequence: WP_058645630.1. A fragment of MARTX cysteine protease domain lacking the C-terminal beta-flap. The N-terminal GSAMGS is a linker sequence from the plasmid vector for the cleavable His-tag. Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Gene: rtxa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-IHP / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: .1 M sodium acetate pH 4.0, 25% PEG 3350, 0.2 M ammonium acetate, and 2.5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å |
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: 2.2→50 Å / Num. obs: 18979 / % possible obs: 99.7 % / Redundancy: 11.6 % / Biso Wilson estimate: 36.53 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 43.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 12 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 918 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.4 Å / SU ML: 0.2673 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5772 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→32.4 Å
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Refine LS restraints |
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LS refinement shell |
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