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- PDB-9eng: Structure of K.pneumoniae LpxH in complex with EBL-3218 -

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Basic information

Entry
Database: PDB / ID: 9eng
TitleStructure of K.pneumoniae LpxH in complex with EBL-3218
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / Lipid A biosynthesis pathway Endotoxin UDP-diacyl-glucosamine lipid X Gram-negative bacteria Antibiotic 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: 2.2 Å
AuthorsSooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors.
Authors: Benediktsdottir, A. / Sooriyaarachchi, S. / Cao, S. / Ottosson, N.E. / Lindstrom, S. / Lundgren, B. / Kloditz, K. / Lola, D. / Bobileva, O. / Loza, E. / Hughes, D. / Jones, T.A. / Mowbray, S. ...Authors: Benediktsdottir, A. / Sooriyaarachchi, S. / Cao, S. / Ottosson, N.E. / Lindstrom, S. / Lundgren, B. / Kloditz, K. / Lola, D. / Bobileva, O. / Loza, E. / Hughes, D. / Jones, T.A. / Mowbray, S.L. / Zamaratski, E. / Sandstrom, A. / Karlen, A.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_entry_details.has_protein_modification

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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)28,7024
Polymers28,0091
Non-polymers6933
Water1086
1
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules

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


  • defined by author
  • Evidence: I have defined the 12th symmetry operation to create a dimer but seems to not work. I also tried the rotation transpose but it does not work either. Do you want a cartesian coordinates ...Evidence: I have defined the 12th symmetry operation to create a dimer but seems to not work. I also tried the rotation transpose but it does not work either. Do you want a cartesian coordinates operator or an international tables space-group operator?
  • 57.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)57,4058
Polymers56,0182
Non-polymers1,3876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)60.604, 60.604, 287.228
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1H55 / ~{N}-[4-[4-[3,5-bis(chloranyl)phenyl]piperazin-1-yl]sulfonylphenyl]-3-(methylsulfonylamino)benzamide


Mass: 583.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24Cl2N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 1 6.5 50 % Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17034 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 21.6
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 17034 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.939 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30274 831 4.9 %RANDOM
Rwork0.23565 ---
obs0.23883 16103 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å2-0 Å2
3----3.06 Å2
Refinement stepCycle: 1 / Resolution: 2.2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 39 6 1870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161696
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.6372612
X-RAY DIFFRACTIONr_angle_other_deg0.4521.5723928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4545226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.003516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53210297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
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_it4.9216.091910
X-RAY DIFFRACTIONr_mcbond_other4.9216.091910
X-RAY DIFFRACTIONr_mcangle_it6.6889.1181134
X-RAY DIFFRACTIONr_mcangle_other6.6879.1181135
X-RAY DIFFRACTIONr_scbond_it4.8456.3181019
X-RAY DIFFRACTIONr_scbond_other4.7656.318978
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5299.3731421
X-RAY DIFFRACTIONr_long_range_B_refined8.47971.7232050
X-RAY DIFFRACTIONr_long_range_B_other8.31271.972000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 65 -
Rwork0.349 1148 -
obs--100 %

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