+Open data
-Basic information
Entry | Database: PDB / ID: 8qk2 | ||||||
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Title | Structure of K.pneumoniae LpxH in complex with EBL-3339 | ||||||
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: 1.95 Å | ||||||
Authors | Sooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L. | ||||||
Funding support | Sweden, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qk2.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qk2.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qk2_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8qk2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8qk2_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 8qk2_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/8qk2 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/8qk2 | HTTPS FTP |
-Related structure data
Related structure data | 8qjzC 8qk5C 8qk9C 8qkaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-VTF / ~{ | Mass: 569.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N7O5S2 / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density meas: 47 Mg/m3 / Density % sol: 54.07 % / Description: Bipyramidal Crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: Morpheus III screen, G6 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 50 % Precipitant Mix 2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 21114 / % possible obs: 88.5 % / Redundancy: 20 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.028 / Rrim(I) all: 0.094 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 1.672 / Num. unique obs: 21114 / CC1/2: 0.792 / Rpim(I) all: 0.507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.59 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.787 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→29.96 Å
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