+Open data
-Basic information
Entry | Database: PDB / ID: 8qka | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of K. pneumoniae LpxH in complex with JEDI-852 | ||||||
Components | UDP-2,3-diacylglucosamine hydrolase | ||||||
Keywords | HYDROLASE / Lipid A biosynthesis pathway Endotoxin UDP-diacyl-glucosamine lipid X Gram-negative bacteria Lipopolysaccharides | ||||||
Function / homology | Function and homology information UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | ||||||
Funding support | Sweden, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria. Authors: Huseby, D.L. / Cao, S. / Zamaratski, E. / Sooriyaarachchi, S. / Ahmad, S. / Bergfors, T. / Krasnova, L. / Pelss, J. / Ikaunieks, M. / Loza, E. / Katkevics, M. / Bobileva, O. / Cirule, H. / ...Authors: Huseby, D.L. / Cao, S. / Zamaratski, E. / Sooriyaarachchi, S. / Ahmad, S. / Bergfors, T. / Krasnova, L. / Pelss, J. / Ikaunieks, M. / Loza, E. / Katkevics, M. / Bobileva, O. / Cirule, H. / Gukalova, B. / Grinberga, S. / Backlund, M. / Simoff, I. / Leber, A.T. / Berruga-Fernandez, T. / Antonov, D. / Konda, V.R. / Lindstrom, S. / Olanders, G. / Brandt, P. / Baranczewski, P. / Vingsbo Lundberg, C. / Liepinsh, E. / Suna, E. / Jones, T.A. / Mowbray, S.L. / Hughes, D. / Karlen, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qka.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qka.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 8qka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qka_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qka_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8qka_validation.xml.gz | 11 KB | Display | |
Data in CIF | 8qka_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/8qka ftp://data.pdbj.org/pub/pdb/validation_reports/qk/8qka | HTTPS FTP |
-Related structure data
Related structure data | 8qjzC 8qk2C 8qk5C 8qk9C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28008.943 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: lpxH / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: A6T5R0 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-VTK / | Mass: 451.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O5S2 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.34 % / Description: Bipyramidal shaped crystal |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: Morpheus III G12 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 3 8.5 50 % Precipitant Mix 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918401 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918401 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 21782 / % possible obs: 100 % / Redundancy: 36 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.024 / Rrim(I) all: 0.112 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1523 / CC1/2: 0.98 / Rpim(I) all: 0.177 / Rrim(I) all: 0.771 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.564 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.865 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→29.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|