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- PDB-4pkr: Anthrax toxin lethal factor with bound small molecule inhibitor 10 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pkr | ||||||||||||
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Title | Anthrax toxin lethal factor with bound small molecule inhibitor 10 | ||||||||||||
![]() | Lethal factor | ||||||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / structural dynamics / ligand-induced conformational change / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Maize, K.M. / De la Mora, T. / Finzel, B.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.6 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pkqC ![]() 4pksC ![]() 4pktC ![]() 4pkuC ![]() 4pkvC ![]() 4pkwC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: P15917, anthrax lethal factor endopeptidase |
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-Non-polymers , 5 types, 312 molecules ![](data/chem/img/2ZL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-2ZL / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 30, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→44.89 Å / Num. obs: 27371 / % possible obs: 95.4 % / Redundancy: 6.62 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.12 / Net I/σ(I): 8.7 / Num. measured all: 182509 / Scaling rejects: 1369 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 2.2→39 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.93 / 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: 83.52 Å2 / Biso mean: 30.4009 Å2 / Biso min: 13.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→39 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: 10
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