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Open data
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Basic information
Entry | Database: PDB / ID: 5d1u | ||||||
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Title | Anthrax toxin lethal factor with hydroxamic acid inhibitor | ||||||
![]() | 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. / Finzel, B.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the S2' Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. Authors: Kurbanov, E.K. / Chiu, T.L. / Solberg, J. / Francis, S. / Maize, K.M. / Fernandez, J. / Johnson, R.L. / Hawkinson, J.E. / Walters, M.A. / Finzel, B.C. / Amin, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.2 KB | Display | ![]() |
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PDB format | ![]() | 82.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wf6C ![]() 5d1sC ![]() 5d1tC ![]() 1yqyS S: Starting model for refinement 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
#1: Protein | Mass: 60436.047 Da / Num. of mol.: 1 / Fragment: residues 298-809 / Mutation: A299S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P15917, anthrax lethal factor endopeptidase |
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#2: Chemical | ChemComp-56P / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.05 % |
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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.85→77.293 Å / Num. obs: 15129 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 52.08 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.1 / Num. measured all: 96780 | |||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YQY Resolution: 2.8503→39.632 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.24 / 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: 121.13 Å2 / Biso mean: 51.3988 Å2 / Biso min: 20.71 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8503→39.632 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: 5 / % reflection obs: 100 %
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