[English] 日本語
Yorodumi- PDB-1zxv: X-Ray Crystal Structure of the Anthrax Lethal Factor Bound to a S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zxv | ||||||
---|---|---|---|---|---|---|---|
Title | X-Ray Crystal Structure of the Anthrax Lethal Factor Bound to a Small Molecule Inhibitor, BI-MFM3, 3-{5-[5-(4-Chloro-phenyl)-furan-2-ylmethylene]-4-oxo-2-thioxo-thiazolidin-3-yl}-propionic acid. | ||||||
Components | lethal factor | ||||||
Keywords | HYDROLASE / Anthrax Toxin Lethal Factor / protein and small molecule inhibitor complex / zinc metalloproteinase | ||||||
Function / homology | Function and homology information : / metallopeptidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Wong, T.Y. / Liddington, R.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Efficient synthetic inhibitors of anthrax lethal factor. Authors: Forino, M. / Johnson, S. / Wong, T.Y. / Rozanov, D.V. / Savinov, A.Y. / Li, W. / Fattorusso, R. / Becattini, B. / Orry, A.J. / Jung, D. / Abagyan, R.A. / Smith, J.W. / Alibek, K. / ...Authors: Forino, M. / Johnson, S. / Wong, T.Y. / Rozanov, D.V. / Savinov, A.Y. / Li, W. / Fattorusso, R. / Becattini, B. / Orry, A.J. / Jung, D. / Abagyan, R.A. / Smith, J.W. / Alibek, K. / Liddington, R.C. / Strongin, A.Y. / Pellecchia, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zxv.cif.gz | 301.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zxv.ent.gz | 245.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zxv_validation.pdf.gz | 968 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zxv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1zxv_validation.xml.gz | 56.7 KB | Display | |
Data in CIF | 1zxv_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zxv ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zxv | HTTPS FTP |
-Related structure data
Related structure data | 1j7nS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 90356.812 Da / Num. of mol.: 2 / Fragment: Mature peptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef / Plasmid: pSJ119 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441 References: GenBank: 143144, UniProt: Q52NH3*PLUS, anthrax lethal factor endopeptidase #2: Chemical | #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.73 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 22, 2004 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→49 Å / Num. all: 160988 / Num. obs: 70243 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Rsym value: 0.074 / Net I/σ(I): 13.29 |
Reflection shell | Resolution: 2.67→2.77 Å / Mean I/σ(I) obs: 1.76 / Num. unique all: 70243 / Rsym value: 0.5945 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1J7N Resolution: 2.67→49 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→49 Å
|