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- PDB-6i46: Structure of P. aeruginosa LpxC with compound 8: (2RS)-4-(5-(2-Fl... -

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Basic information

Entry
Database: PDB / ID: 6i46
TitleStructure of P. aeruginosa LpxC with compound 8: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-2-oxooxazol-3(2H)-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding / membrane
Similarity search - Function
UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-H2N / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSurivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. ...Surivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Enderlin-Paput, M. / Lange, R. / Bur, D. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Hermann, C. / Locher, H.H. / Seiler, P. / Mac Sweeney, A. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria.
Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. ...Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Herrmann, C. / Seiler, P. / Enderlin-Paput, M. / Mac Sweeney, A. / Wicki, M. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
History
DepositionNov 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7074
Polymers33,1471
Non-polymers5603
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint0 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.754, 66.614, 62.926
Angle α, β, γ (deg.)90.000, 90.415, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase / UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase


Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa LESB58 (bacteria)
Gene: lpxC, PLES_47851 / Production host: Escherichia coli (E. coli)
References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-H2N / (2~{R})-4-[5-(2-fluoranyl-4-methoxy-phenyl)-2-oxidanylidene-1,3-oxazol-3-yl]-2-methyl-2-methylsulfonyl-~{N}-oxidanyl-butanamide


Mass: 402.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19FN2O7S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26-30% (w/v) PEG 4000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→35.8 Å / Num. obs: 55874 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 1.76 % / CC1/2: 0.995 / Rrim(I) all: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 1.75→1.86 Å / Mean I/σ(I) obs: 0.9 / CC1/2: 0.439 / Rrim(I) all: 1.039 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238 2018/15/10refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ves

2ves


Resolution: 1.75→35.779 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.196 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2234 1487 -
Rwork0.1784 --
all0.181 --
obs-29727 99.515 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.375 Å2-0 Å20.446 Å2
2---0.842 Å2-0 Å2
3---0.461 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 34 138 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172232
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6573213
X-RAY DIFFRACTIONr_angle_other_deg1.3861.5875146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48522.101119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5111516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined0.2020.2417
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22172
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21180
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2120
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0820.28
X-RAY DIFFRACTIONr_nbd_other0.2060.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.212
X-RAY DIFFRACTIONr_mcbond_it1.9742.4651195
X-RAY DIFFRACTIONr_mcbond_other1.9662.4631194
X-RAY DIFFRACTIONr_mcangle_it2.7423.6891492
X-RAY DIFFRACTIONr_mcangle_other2.7453.6911493
X-RAY DIFFRACTIONr_scbond_it3.0622.8521179
X-RAY DIFFRACTIONr_scbond_other3.0612.8531180
X-RAY DIFFRACTIONr_scangle_it4.6394.131721
X-RAY DIFFRACTIONr_scangle_other4.6384.1321722
X-RAY DIFFRACTIONr_lrange_it5.73529.7322539
X-RAY DIFFRACTIONr_lrange_other5.71929.5672519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.75-1.7950.3281100.32092222798.87740.299
1.795-1.8450.2761060.2682002211099.90520.267
1.845-1.8980.2631050.251991209799.95230.246
1.898-1.9560.2791000.2341900200799.65120.226
1.956-2.020.273970.2151846195199.590.203
2.02-2.0910.228950.2041811190899.89520.189
2.091-2.170.256910.1851722181499.94490.169
2.17-2.2580.211890.178169017791000.163
2.258-2.3580.246840.1621603168999.88160.143
2.358-2.4730.196800.1521530161199.93790.134
2.473-2.6060.254770.1611461154299.74060.141
2.606-2.7640.247740.1791395147499.66080.158
2.764-2.9540.241680.1651294136899.56140.151
2.954-3.190.205630.1651207127599.60780.156
3.19-3.4920.201590.1661125119299.32890.163
3.492-3.9020.201530.162994106498.40230.167
3.902-4.50.207470.14589895798.74610.158
4.5-5.4980.165400.16475079799.12170.183
5.498-7.720.235310.17958663397.47240.202
7.72-45.7430.18180.17534137196.76550.222

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