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- PDB-6i49: Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i49 | ||||||
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Title | Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy-2-methyl-2-(methylsulfonyl)-4(6((4(morpholinomethyl)phenyl)ethynyl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)yl)butanamide | ||||||
![]() | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
![]() | HYDROLASE / Inhibitor | ||||||
Function / homology | ![]() UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Surivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. ...Surivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Enderlin-Paput, M. / Lange, R. / Bur, D. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Hermann, C. / Locher, H.H. / Seiler, P. / Mac Sweeney, A. / Hubschwerlen, C. / Ritz, D. / Rueedi, G. | ||||||
![]() | ![]() Title: Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria. Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. ...Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Herrmann, C. / Seiler, P. / Enderlin-Paput, M. / Mac Sweeney, A. / Wicki, M. / Hubschwerlen, C. / Ritz, D. / Rueedi, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 855.3 KB | Display | ![]() |
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Full document | ![]() | 862 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i46C ![]() 6i47C ![]() 6i48C ![]() 6i4aC ![]() 2vesS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A B) |
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Components
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 2 / Mutation: C40S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lpxC, PLES_47851 / Production host: ![]() ![]() References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.1 M sodium acetate pH 4.6, 7 % (w/v) PEG 400, 7 % (w/v) PEG 500 MME, 7 % (w/v) PEG 600, 7 % (w/v) PEG 1000, 5 % (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→43.122 Å / Num. obs: 74154 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.94→2.06 Å / Mean I/σ(I) obs: 2.1 / CC1/2: 0.725 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ves Resolution: 1.94→43.122 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.595 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.173 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.151 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→43.122 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: 20
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