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- PDB-8s7f: Crystal structure of Escherichia coli LpxH in complex with EBL-2805 -

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Basic information

Entry
Database: PDB / ID: 8s7f
TitleCrystal structure of Escherichia coli LpxH in complex with EBL-2805
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / Lipid A biosynthesis pathway Endotoxin UDP-diacyl-glucosamine lipid X Gram-negative bacteria Antibiotic Inhibitor 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSooriyaarachchi, S. / Mowbray, S.L. / Bergfors, T. / Jones, T.A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic Research 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 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 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)28,4254
Polymers27,7181
Non-polymers7073
Water4,161231
1
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,8518
Polymers55,4362
Non-polymers1,4156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)79.563, 52.271, 86.355
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27717.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxH, c0639 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / Variant (production host): BL21-AI
References: UniProt: Q8FK47, UDP-2,3-diacylglucosamine diphosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-A1H5P / N-[4-[4-[3,5-bis(chloranyl)phenyl]piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide


Mass: 597.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26Cl2N4O5S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.02 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3% w/v CHAPS, 3% w/v CHAPSO, 3% w/v Sodium glycocholate hydrate, 3% w/v Taurocholic acid sodium salt hydrate Tris (base); BICINE, pH 8.5 40% v/v Ethylene glycol 20 % w/v PEG 8000

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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: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.6→80.5 Å / Num. obs: 43761 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 43761 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→80.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.347 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20576 2269 5.2 %RANDOM
Rwork0.1844 ---
obs0.18548 41491 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.07 Å2
2--0.72 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.6→80.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 40 231 2102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161730
X-RAY DIFFRACTIONr_angle_refined_deg1.0411.6542606
X-RAY DIFFRACTIONr_angle_other_deg0.3821.5774002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.21514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57410305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022181
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_it0.8941.594922
X-RAY DIFFRACTIONr_mcbond_other0.8941.594922
X-RAY DIFFRACTIONr_mcangle_it1.5332.381149
X-RAY DIFFRACTIONr_mcangle_other1.5332.3821150
X-RAY DIFFRACTIONr_scbond_it1.1991.7561007
X-RAY DIFFRACTIONr_scbond_other1.1951.757965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9292.5741398
X-RAY DIFFRACTIONr_long_range_B_refined3.78621.7742202
X-RAY DIFFRACTIONr_long_range_B_other3.58520.8632077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 176 -
Rwork0.232 3052 -
obs--99.94 %

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