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- PDB-7pzv: LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group ... -

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Basic information

Entry
Database: PDB / ID: 7pzv
TitleLpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Elastase / Inhibitor / Fluoroproline / Zinc-Binding Group / Antibiotic / Multidrug-Resistant Gram-Negative Bacteria
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
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-9DO / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRyan, M.D. / Pallin, T.D. / Lamers, M.B.A.C. / Leonard, P.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria
Authors: Ryan, M.D. / Pallin, T.D. / Mullins, T. / Blench, T. / Fraser, I. / Dallow, J. / Ahmed, N. / Ellwood, C. / Gaines, S. / Flores, J. / Blackwell, Y. / Garcia, C.T. / Spence, G. / Reeve, A. / ...Authors: Ryan, M.D. / Pallin, T.D. / Mullins, T. / Blench, T. / Fraser, I. / Dallow, J. / Ahmed, N. / Ellwood, C. / Gaines, S. / Flores, J. / Blackwell, Y. / Garcia, C.T. / Spence, G. / Reeve, A. / Panchal, T. / Dominguez-Fernandez, B. / Leonard, P.M. / Lamers, M.B.A.C. / Arduin, A. / Fotinou, C. / Gancia, E. / Clark, D.E. / Bush, E. / Betts, J. / Richards, C. / Rea-Davies, T. / Keefe, A.D. / Zhang, Y. / Soutter, H.T. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Habeshian, S. / Hunt, A. / Sigel, E.A. / Troast, D.M. / DeJonge, B.L.M.
History
DepositionOct 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4993
Polymers34,8571
Non-polymers6422
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.585, 66.965, 62.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 34857.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lpxC, envA, PA4406 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P47205, 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-9DO / (2S,4S)-N-[(3R,5R)-1-cyclopropylcarbonyl-5-[[[4-[2-[4-[(1S)-2-methoxy-1-oxidanyl-ethyl]phenyl]ethynyl]phenyl]carbonylamino]methyl]pyrrolidin-3-yl]-4-fluoranyl-pyrrolidine-2-carboxamide / (2S,4S)-N-((3R,5R)-1-(cyclopropanecarbonyl)-5-((4-((4-((S)-1-hydroxy-2-methoxyethyl)phenyl)ethynyl)benzamido)methyl)pyrrolidin-3-yl)-4-fluoropyrrolidine-2-carboxamide


Mass: 576.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37FN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 26% PEG 3350, 0.2 M NA ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.92→62.87 Å / Num. obs: 22650 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.976 / Net I/σ(I): 3.9
Reflection shellResolution: 1.92→1.97 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1628 / CC1/2: 0.682

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VES

2ves


Resolution: 1.92→62.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.199 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24832 1158 5.1 %RANDOM
Rwork0.19919 ---
obs0.2016 21476 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-1.82 Å2
2---1.32 Å2-0 Å2
3---2.1 Å2
Refinement stepCycle: 1 / Resolution: 1.92→62.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 43 169 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172241
X-RAY DIFFRACTIONr_angle_refined_deg1.611.6643213
X-RAY DIFFRACTIONr_angle_other_deg1.371.6015179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4375294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56622.231121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89515399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0731516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
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_it1.3811.6561182
X-RAY DIFFRACTIONr_mcbond_other1.3721.6531181
X-RAY DIFFRACTIONr_mcangle_it2.2112.4721474
X-RAY DIFFRACTIONr_mcangle_other2.2132.4741475
X-RAY DIFFRACTIONr_scbond_it2.0871.9481192
X-RAY DIFFRACTIONr_scbond_other2.0871.951193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2912.8281737
X-RAY DIFFRACTIONr_long_range_B_refined5.50531.9769983
X-RAY DIFFRACTIONr_long_range_B_other5.40831.8329888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 114 -
Rwork0.303 1587 -
obs--99.71 %

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