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- PDB-8qjz: Crystal structure of E. coli LpxH in complex with lipid X -

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Basic information

Entry
Database: PDB / ID: 8qjz
TitleCrystal structure of E. coli LpxH in complex with lipid X
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / Lipid A biosynthesis pathway Endotoxin UDP-diacyl-glucosamine Lipid X Gram-negative bacteria Lipopolysaccharides HYDROLASE
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
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
Chem-LP5 / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6854
Polymers27,8631
Non-polymers8223
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-17 kcal/mol
Surface area11320 Å2
Unit cell
Length a, b, c (Å)123.827, 81.392, 33.127
Angle α, β, γ (deg.)90.00, 100.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27863.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxH / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: A0A066QL39
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.57 % / Description: bipyramidal crystal
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Morpheus III (G7) 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 50 % Precipitant Mix 3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 11, 2019
Details: quasi-periodic elliptically polarizing undulator (qEPU)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.35→67.6 Å / Num. obs: 70366 / % possible obs: 99 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.35→1.42 Å / Num. unique obs: 9911 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.916 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18733 3468 4.9 %RANDOM
Rwork0.17146 ---
obs0.17224 66887 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.599 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---1.4 Å20 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 50 233 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122011
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161819
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.6522707
X-RAY DIFFRACTIONr_angle_other_deg0.4651.5734216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.337515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81710328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
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_it1.191.685962
X-RAY DIFFRACTIONr_mcbond_other1.1731.684962
X-RAY DIFFRACTIONr_mcangle_it1.8372.5281199
X-RAY DIFFRACTIONr_mcangle_other1.8372.5291200
X-RAY DIFFRACTIONr_scbond_it1.9681.9441049
X-RAY DIFFRACTIONr_scbond_other1.9451.9111000
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9332.781449
X-RAY DIFFRACTIONr_long_range_B_refined4.32725.682229
X-RAY DIFFRACTIONr_long_range_B_other4.13922.1232147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.384 Å
RfactorNum. reflection% reflection
Rfree0.297 255 -
Rwork0.282 4713 -
obs--95.04 %

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