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- PDB-7ci4: Crystal structure of P.aeruginosa LpxC in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7ci4
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-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-FXU / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMima, M. / Baker, L.M. / Surgenor, A. / Robertson, A.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity.
Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / ...Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / Ohtake, N. / Angove, H. / Baker, L. / Harris, R. / Macias, A. / Robertson, A. / Surgenor, A. / Watanabe, H. / Nakano, K. / Mima, M. / Iwamoto, K. / Okada, A. / Takata, I. / Hitaka, K. / Tanaka, A. / Fujita, K. / Sugiyama, H. / Hubbard, R.E.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,22410
Polymers66,2932
Non-polymers9318
Water6,503361
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6125
Polymers33,1471
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13580 Å2
MethodPISA
2
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6125
Polymers33,1471
Non-polymers4654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.367, 51.180, 96.763
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / 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 (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 5 types, 369 molecules

#2: Chemical ChemComp-FXU / (2R)-2-azanyl-4-methylsulfonyl-N-[3-(trifluoromethyloxy)phenyl]butanamide


Mass: 340.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15F3N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 20 % w/v Polyethylene glycol 6,000 100 mM HEPES pH 7.0 200 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→23.31 Å / Num. obs: 41967 / % possible obs: 96.9 % / Redundancy: 7.47 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.32 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4073 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UHM

3uhm


Resolution: 2→23.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.551 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24088 2150 5.1 %RANDOM
Rwork0.18685 ---
obs0.1896 39816 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.02 Å2
2--0.07 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2→23.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 50 361 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174513
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6526444
X-RAY DIFFRACTIONr_angle_other_deg1.3231.58710427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7425592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73822.031256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14115826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7591536
X-RAY DIFFRACTIONr_chiral_restr0.0720.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
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_it2.7733.2232377
X-RAY DIFFRACTIONr_mcbond_other2.773.2212376
X-RAY DIFFRACTIONr_mcangle_it4.0834.8172966
X-RAY DIFFRACTIONr_mcangle_other4.0824.8212967
X-RAY DIFFRACTIONr_scbond_it3.6193.7782388
X-RAY DIFFRACTIONr_scbond_other3.6143.7772383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6565.4873472
X-RAY DIFFRACTIONr_long_range_B_refined7.48638.3645185
X-RAY DIFFRACTIONr_long_range_B_other7.47138.2755162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 138 -
Rwork0.261 2842 -
obs--93.83 %

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