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- PDB-8qk5: Structure of K. pneumoniae LpxH in complex with EBL-3647 -

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Basic information

Entry
Database: PDB / ID: 8qk5
TitleStructure of K. pneumoniae LpxH in complex with EBL-3647
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / 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 / extrinsic component of plasma membrane / lipid A biosynthetic process / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: 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
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7874
Polymers28,0091
Non-polymers7783
Water86548
1
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules

A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5738
Polymers56,0182
Non-polymers1,5556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2250 Å2
ΔGint-33 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.418, 60.418, 287.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UDP-2,3-diacylglucosamine hydrolase


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 BL21 (bacteria) / Variant (production host): AI / References: UniProt: A6T5R0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-VN6 / 5-[[3-(aminomethyl)azetidin-1-yl]methyl]-N-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide


Mass: 667.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N9O5S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.64 % / Description: bipyramidal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: Morpheus III - G11 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 3 8.5 50 % Precipitant Mix 3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 23964 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 23964 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.083 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28192 1219 5.1 %RANDOM
Rwork0.23973 ---
obs0.24195 22624 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.005 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 48 48 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161698
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.6352652
X-RAY DIFFRACTIONr_angle_other_deg0.4661.5763934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.54515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20910297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2554.902914
X-RAY DIFFRACTIONr_mcbond_other4.254.902914
X-RAY DIFFRACTIONr_mcangle_it5.4337.3151139
X-RAY DIFFRACTIONr_mcangle_other5.4317.3191140
X-RAY DIFFRACTIONr_scbond_it4.4525.211042
X-RAY DIFFRACTIONr_scbond_other4.4255.224991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9657.7151440
X-RAY DIFFRACTIONr_long_range_B_refined7.61856.6712135
X-RAY DIFFRACTIONr_long_range_B_other7.56656.8912058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 99 -
Rwork0.38 1592 -
obs--99.94 %

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