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Yorodumi- PDB-6i4a: Structure of P. aeruginosa LpxC with compound 18d: (2R)-N-Hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i4a | ||||||
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Title | Structure of P. aeruginosa LpxC with compound 18d: (2R)-N-Hydroxy-4-(6-((1-(hydroxymethyl)cyclopropyl)buta-1,3-diyn-1-yl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl)-2-methyl-2-(methylsulfonyl)butanamide | ||||||
Components | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
Keywords | HYDROLASE / Inhibitor | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa LESB58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å | ||||||
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. ...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. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i4a.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i4a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6i4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i4a_validation.pdf.gz | 768 KB | Display | wwPDB validaton report |
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Full document | 6i4a_full_validation.pdf.gz | 770.7 KB | Display | |
Data in XML | 6i4a_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6i4a_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4a ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4a | HTTPS FTP |
-Related structure data
Related structure data | 6i46C 6i47C 6i48C 6i49C 2vesS S: Starting model for refinement 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
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa LESB58 (bacteria) Gene: lpxC, PLES_47851 / Production host: Escherichia coli (E. coli) References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-H2Q / ( |
#4: 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: 46.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20 % PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→36.003 Å / Num. obs: 14233 / % possible obs: 99.7 % / Redundancy: 3.45 % / CC1/2: 0.993 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.25→2.39 Å / Mean I/σ(I) obs: 1.2 / CC1/2: 0.46 / Rrim(I) all: 1.25 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ves Resolution: 2.251→36.003 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 12.012 / SU ML: 0.273 / Cross valid method: FREE R-VALUE / ESU R: 0.426 / ESU R Free: 0.276 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: 27.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.251→36.003 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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