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

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Basic information

Entry
Database: PDB / ID: 7cib
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
2-oxidanyl-4-phenyl-benzoic acid / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6616
Polymers33,1471
Non-polymers5145
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.780, 75.800, 95.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-FYR / 2-oxidanyl-4-phenyl-benzoic acid


Mass: 214.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 4K 0.2M MgCl2 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→35.243 Å / Num. obs: 28572 / % possible obs: 83.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.8
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2003 / % possible all: 80.7

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Processing

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

3uhm


Resolution: 1.61→35.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.617 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21772 1460 5.1 %RANDOM
Rwork0.17794 ---
obs0.18002 27088 82.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.44 Å2
Refinement stepCycle: 1 / Resolution: 1.61→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 29 213 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132432
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172322
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.653292
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5825358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03721.493134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9511521
X-RAY DIFFRACTIONr_chiral_restr0.080.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02536
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_it1.521.9571205
X-RAY DIFFRACTIONr_mcbond_other1.5041.9551204
X-RAY DIFFRACTIONr_mcangle_it2.222.931507
X-RAY DIFFRACTIONr_mcangle_other2.2272.9321508
X-RAY DIFFRACTIONr_scbond_it2.5482.31227
X-RAY DIFFRACTIONr_scbond_other2.5482.3021228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7183.3321781
X-RAY DIFFRACTIONr_long_range_B_refined5.29224.0722665
X-RAY DIFFRACTIONr_long_range_B_other5.1523.7062618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 103 -
Rwork0.309 1892 -
obs--79.7 %

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