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- PDB-7den: Crystal structure of P.aeruginosa LpxC in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7den
TitleCrystal structure of P.aeruginosa LpxC in complex with inhibitor
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / UDP-3-O-acyl-N-acetylglucosamine deacetylase EnvA / LpxC / Pseudomonas aeruginosa
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / 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-H4R / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMima, M. / Ushiyama, F. / Takashima, H.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532.
Authors: Ushiyama, F. / Takashima, H. / Matsuda, Y. / Ogata, Y. / Sasamoto, N. / Kurimoto-Tsuruta, R. / Ueki, K. / Tanaka-Yamamoto, N. / Endo, M. / Mima, M. / Fujita, K. / Takata, I. / Tsuji, S. / ...Authors: Ushiyama, F. / Takashima, H. / Matsuda, Y. / Ogata, Y. / Sasamoto, N. / Kurimoto-Tsuruta, R. / Ueki, K. / Tanaka-Yamamoto, N. / Endo, M. / Mima, M. / Fujita, K. / Takata, I. / Tsuji, S. / Yamashita, H. / Okumura, H. / Otake, K. / Sugiyama, H.
History
DepositionNov 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,6733
Polymers33,1471
Non-polymers5262
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13470 Å2
Unit cell
Length a, b, c (Å)36.150, 66.310, 63.520
Angle α, β, γ (deg.)90.00, 90.75, 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: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-H4R / 4-[(1~{R},5~{S})-6-[2-[4-[3-[[2-[(1~{S})-1-oxidanylethyl]imidazol-1-yl]methyl]-1,2-oxazol-5-yl]phenyl]ethynyl]-3-azabicyclo[3.1.0]hexan-3-yl]butanoic acid


Mass: 460.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.16 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5
Details: 20 % w/v Polyethylene glycol 8,000, 100 mM CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→45.87 Å / Num. obs: 18557 / % possible obs: 99.7 % / Redundancy: 3.47 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.43
Reflection shellResolution: 2.07→2.12 Å / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 2725

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UHM

3uhm


Resolution: 2.07→45.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.794 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21542 927 5 %RANDOM
Rwork0.16623 ---
obs0.16881 17614 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: 28.197 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å2-0.42 Å2
2---0.24 Å2-0 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.07→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 35 182 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192378
X-RAY DIFFRACTIONr_bond_other_d0.0020.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9813215
X-RAY DIFFRACTIONr_angle_other_deg1.11235195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72524.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46415409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6781517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02488
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_it2.1732.5511178
X-RAY DIFFRACTIONr_mcbond_other2.1722.551177
X-RAY DIFFRACTIONr_mcangle_it3.0493.8071469
X-RAY DIFFRACTIONr_mcangle_other3.0493.8091470
X-RAY DIFFRACTIONr_scbond_it3.4923.0371200
X-RAY DIFFRACTIONr_scbond_other3.493.0371201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.334.3871744
X-RAY DIFFRACTIONr_long_range_B_refined7.63451.75711235
X-RAY DIFFRACTIONr_long_range_B_other7.59151.6411133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.119 Å
RfactorNum. reflection% reflection
Rfree0.276 69 -
Rwork0.229 1316 -
obs--100 %

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