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Yorodumi- PDB-4wx5: pore-forming thermostable direct hemolysin from Grimontia hollisae -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wx5 | ||||||
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Title | pore-forming thermostable direct hemolysin from Grimontia hollisae | ||||||
Components | Hemolysin, heat labile | ||||||
Keywords | TOXIN / thermostable direct hemolysin / TDH / oligomerization | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Grimontia hollisae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.302 Å | ||||||
Authors | Wang, Y.-K. / Wu, T.-K. / Li, T.-H.T. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To be published Title: Multiple pleomorphic tetramers of pore-forming thermostable direct hemolysin from Grimontia hollisae in exerting membrane binding and hemolytic activity Authors: Wang, Y.-K. / Huang, S.-C. / Huang, W.-T. / Chang, C.-Y. / Kuo, T.-M. / Yip, B.-S. / Wu, T.-K. / Li, T.-H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wx5.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wx5.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wx5_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 4wx5_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 4wx5_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4wx5_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wx5 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wx5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18643.596 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Grimontia hollisae (bacteria) / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pLysS) / References: UniProt: P14711 #2: Water | ChemComp-HOH / | Sequence details | THE AUTHORS USED GRIMONTIA HOLLISAE STRAIN ATCC33564. THE AUTHORS ARE CONVINCED OF THIS SEQUENCE BY ...THE AUTHORS USED GRIMONTIA HOLLISAE STRAIN ATCC33564. THE AUTHORS ARE CONVINCED OF THIS SEQUENCE BY THE ELECTRON DENSITY MAP. | |
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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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28%(v/v) PEG 400, 0.2 M CaCl2, 0.1 M Na-HEPES buffer |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.96379, 0.97904, 0.97920 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2010 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→30 Å / Num. obs: 32500 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 21.8 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 6.7 / % possible all: 97.9 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.302→26.768 Å / FOM work R set: 0.7285 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.48 / Stereochemistry target values: MLHL
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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 max: 80.31 Å2 / Biso mean: 31.36 Å2 / Biso min: 10.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.302→26.768 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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