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Yorodumi- PDB-1pww: Crystal structure of Anthrax Lethal Factor active site mutant pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pww | ||||||
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Title | Crystal structure of Anthrax Lethal Factor active site mutant protein complexed with an optimised peptide substrate in the presence of zinc. | ||||||
Components |
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Keywords | HYDROLASE / Anthrax Toxin / Lethal Factor (active site mutant) / optimised peptide substrate | ||||||
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: 2.8 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 | 1pww.cif.gz | 306.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pww.ent.gz | 248.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pww_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 1pww_full_validation.pdf.gz | 544.2 KB | Display | |
Data in XML | 1pww_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 1pww_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pww ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pww | HTTPS FTP |
-Related structure data
Related structure data | 1pwqC 1pwuC 1pwvC 1j7nS C: citing same article (ref.) 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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3 |
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Unit cell |
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Details | Biological unit is a monomer. |
-Components
#1: Protein | Mass: 90330.836 Da / Num. of mol.: 2 / Mutation: E687C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: LEF OR PXO1-107 / Plasmid: pX01 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441 References: UniProt: P15917, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases #2: Protein/peptide | Mass: 2354.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This optimised peptide substrate was synthesised. #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: 3.6 Å3/Da / Density % sol: 65.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulphate, 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: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 55305 / Num. obs: 55305 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Rsym value: 0.12 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 55305 / Rsym value: 0.408 / % possible all: 86.5 |
Reflection | *PLUS Num. obs: 54931 / % possible obs: 86.8 % / Num. measured all: 94088 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 76 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1J7N Resolution: 2.8→22.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 129540.38 / Data cutoff high rms absF: 129540.38 / 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: 31.6192 Å2 / ksol: 0.359059 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→22.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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