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Yorodumi- PDB-1pwp: Crystal Structure of the Anthrax Lethal Factor complexed with Sma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwp | ||||||
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Title | Crystal Structure of the Anthrax Lethal Factor complexed with Small Molecule Inhibitor NSC 12155 | ||||||
Components | Lethal factor | ||||||
Keywords | HYDROLASE / Anthrax Toxin / Lethal Factor / small molecule inhibitor | ||||||
Function / homology | Function and homology information anthrax lethal factor endopeptidase / host cell cytosol / Uptake and function of anthrax toxins / metalloendopeptidase activity / metallopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wong, T.Y. / Schwarzenbacher, R. / Liddington, R.C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Identification of small molecule inhibitors of anthrax lethal factor. Authors: Panchal, R.G. / Hermone, A.R. / Nguyen, T.L. / Wong, T.Y. / Schwarzenbacher, R. / Schmidt, J. / Lane, D. / McGrath, C. / Turk, B.E. / Burnett, J. / Aman, M.J. / Little, S. / Sausville, E.A. ...Authors: Panchal, R.G. / Hermone, A.R. / Nguyen, T.L. / Wong, T.Y. / Schwarzenbacher, R. / Schmidt, J. / Lane, D. / McGrath, C. / Turk, B.E. / Burnett, J. / Aman, M.J. / Little, S. / Sausville, E.A. / Zaharevitz, D.W. / Cantley, L.C. / Liddington, R.C. / Gussio, R. / Bavari, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pwp.cif.gz | 305.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwp.ent.gz | 247.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pwp_validation.pdf.gz | 858.2 KB | Display | wwPDB validaton report |
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Full document | 1pwp_full_validation.pdf.gz | 914.2 KB | Display | |
Data in XML | 1pwp_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 1pwp_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwp ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwp | HTTPS FTP |
-Related structure data
Related structure data | 1j7nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 90356.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: LEF / Plasmid: pX01 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441 References: UniProt: P15917, anthrax lethal factor endopeptidase #2: Chemical | #3: Chemical | |
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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: 3.58 Å3/Da / Density % sol: 65.62 % | ||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.983 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 56384 / Observed criterion σ(I): 2 / Biso Wilson estimate: 75.7 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.498 / Net I/σ(I): 11.7 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 25 Å / % possible obs: 99.5 % / Num. measured all: 175879 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1J7N Resolution: 2.9→23.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 135641.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.0333 Å2 / ksol: 0.341609 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→23.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.2758 / Rfactor Rwork: 0.2238 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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