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Yorodumi- PDB-4pkw: Anthrax toxin lethal factor with bound small molecule inhibitor GM6001 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pkw | ||||||||||||
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Title | Anthrax toxin lethal factor with bound small molecule inhibitor GM6001 | ||||||||||||
Components | Lethal factor | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / structural dynamics / ligand-induced conformational change / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
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: 1.75 Å | ||||||||||||
Authors | Maize, K.M. / De la Mora, T. / Finzel, B.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding. Authors: Maize, K.M. / Kurbanov, E.K. / De La Mora-Rey, T. / Geders, T.W. / Hwang, D.J. / Walters, M.A. / Johnson, R.L. / Amin, E.A. / Finzel, B.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pkw.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pkw.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pkw_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4pkw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4pkw_validation.xml.gz | 23 KB | Display | |
Data in CIF | 4pkw_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/4pkw ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pkw | HTTPS FTP |
-Related structure data
Related structure data | 4pkqC 4pkrC 4pksC 4pktC 4pkuC 4pkvC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60436.047 Da / Num. of mol.: 1 / Fragment: UNP residues 298-809 / Mutation: A266S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef, pXO1-107, BXA0172, GBAA_pXO1_0172 / Plasmid: pMCSG10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS References: UniProt: P15917, anthrax lethal factor endopeptidase |
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-Non-polymers , 5 types, 392 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-GM6 / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→130.55 Å / Num. obs: 56847 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.8 / Num. measured all: 364950 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→41.381 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
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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: 86.03 Å2 / Biso mean: 27.6386 Å2 / Biso min: 10.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→41.381 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: 21 / % reflection obs: 100 %
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