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Yorodumi- PDB-1pwq: Crystal structure of Anthrax Lethal Factor complexed with Thioace... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwq | ||||||
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Title | Crystal structure of Anthrax Lethal Factor complexed with Thioacetyl-Tyr-Pro-Met-Amide, a metal-chelating peptidyl small molecule inhibitor | ||||||
Components | Lethal factor | ||||||
Keywords | HYDROLASE / Anthrax Toxin / Lethal Factor / metal-chelator / small molecule peptidic 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: 3.52 Å | ||||||
Authors | Wong, T.Y. / Schwarzenbacher, R. / Liddington, R.C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor. Authors: Turk, B.E. / Wong, T.Y. / Schwarzenbacher, R. / Jarrell, E.T. / Leppla, S.H. / Collier, R.J. / Liddington, R.C. / Cantley, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pwq.cif.gz | 305.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwq.ent.gz | 246.6 KB | Display | PDB format |
PDBx/mmJSON format | 1pwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwq ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwq | HTTPS FTP |
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-Related structure data
Related structure data | 1pwuC 1pwvC 1pwwC 1j7nS S: Starting model for refinement C: citing same article (ref.) |
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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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-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: 3.81 Å3/Da / Density % sol: 67.47 % | ||||||||||||||||||||||||||||||
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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 Temperature: 21-29 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.52→30 Å / Num. obs: 28731 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Rsym value: 0.159 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.52→3.6 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.451 / % possible all: 84.9 |
Reflection | *PLUS Highest resolution: 3.5 Å / Num. measured all: 91831 / Rmerge(I) obs: 0.159 |
Reflection shell | *PLUS % possible obs: 84.9 % / Rmerge(I) obs: 0.451 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1J7N Resolution: 3.52→24.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 194801.63 / 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: 10 Å2 / ksol: 0.260498 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.52→24.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.52→3.66 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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