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

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Basic information

Entry
Database: PDB / ID: 7cie
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 / 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-FZ6 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBaker, L.M. / Mima, 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)66,9526
Polymers66,2932
Non-polymers6594
Water3,963220
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4763
Polymers33,1471
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4763
Polymers33,1471
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.118, 50.153, 73.305
Angle α, β, γ (deg.)74.86, 78.03, 63.24
Int Tables number1
Space group name H-MP1

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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.: 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
#2: Chemical ChemComp-FZ6 / (2R)-2-azanyl-3-oxidanyl-N-[3-(trifluoromethyloxy)phenyl]propanamide


Mass: 264.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11F3N2O3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PACT Premier HT-96 F5 (20% PEG3350; 0.2M Sodium Nitrate; 0.1M Bis-Tris Propane pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.15→70.37 Å / Num. obs: 32701 / % possible obs: 98.2 % / Redundancy: 3.24 % / Rmerge(I) obs: 0.1296 / Net I/σ(I): 6.67
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.08 % / Rmerge(I) obs: 0.4803 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 4215 / % possible all: 99.8

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Processing

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

3uhm


Resolution: 2.15→20.53 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.849 / SU B: 8.84 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1597 4.9 %RANDOM
Rwork0.23176 ---
obs0.23496 31104 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.62 Å2-0.82 Å2
2---0.54 Å2-0.57 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 2.15→20.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 38 220 4682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174284
X-RAY DIFFRACTIONr_angle_refined_deg1.711.6446124
X-RAY DIFFRACTIONr_angle_other_deg1.2981.5889886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.85567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43222.181243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91715776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.221533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02978
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_it2.2072.5452280
X-RAY DIFFRACTIONr_mcbond_other2.22.5442279
X-RAY DIFFRACTIONr_mcangle_it3.4923.8062843
X-RAY DIFFRACTIONr_mcangle_other3.4923.8082844
X-RAY DIFFRACTIONr_scbond_it2.4042.8542252
X-RAY DIFFRACTIONr_scbond_other2.4042.8542252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8434.1723282
X-RAY DIFFRACTIONr_long_range_B_refined5.85229.9995022
X-RAY DIFFRACTIONr_long_range_B_other5.84729.9735011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 144 -
Rwork0.308 2307 -
obs--99.88 %

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