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Open data
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Basic information
Entry | Database: PDB / ID: 8e4a | |||||||||
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Title | Pseudomonas LpxC in complex with LPC-233 | |||||||||
![]() | UDP-3-O-acyl-N-acetylglucosamine deacetylase![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Najeeb, J. / Zhou, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Preclinical safety and efficacy characterization of an LpxC inhibitor against Gram-negative pathogens. Authors: Zhao, J. / Cochrane, C.S. / Najeeb, J. / Gooden, D. / Sciandra, C. / Fan, P. / Lemaitre, N. / Newns, K. / Nicholas, R.A. / Guan, Z. / Thaden, J.T. / Fowler Jr., V.G. / Spasojevic, I. / ...Authors: Zhao, J. / Cochrane, C.S. / Najeeb, J. / Gooden, D. / Sciandra, C. / Fan, P. / Lemaitre, N. / Newns, K. / Nicholas, R.A. / Guan, Z. / Thaden, J.T. / Fowler Jr., V.G. / Spasojevic, I. / Sebbane, F. / Toone, E.J. / Duncan, C. / Gammans, R. / Zhou, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.4 KB | Display | ![]() |
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PDB format | ![]() | 108.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3p3eS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A072ZC86, ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-UFX / |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.15 mM protein, 0.6 mM LPC-233, 12.5 mM HEPES (pH 7.1), 25 mM NaCl, 1 mM TCEP, 0.085 M sodium acetate, 0.0425 M Tris HCl pH 8.5, 12.75% PEG 4000, 7.5% glycerol, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.034→46.04 Å / Num. obs: 17695 / % possible obs: 91.08 % / Redundancy: 2.7 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1042 / Net I/σ(I): 10.21 |
Reflection shell | Resolution: 2.034→2.107 Å / Num. unique obs: 1801 / CC1/2: 0.808 / CC star: 0.945 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3P3E Resolution: 2.034→46.04 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.0137 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 18.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.034→46.04 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.0592583112 Å / Origin y: 4.85985865418 Å / Origin z: 76.3989130805 Å
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Refinement TLS group | Selection details: all |