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- PDB-6ih0: Aquifex aeolicus LpxC complex with ACHN-975 -

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Basic information

Entry
Database: PDB / ID: 6ih0
TitleAquifex aeolicus LpxC complex with ACHN-975
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Complex / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex
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
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / 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 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A5F / Chem-A5U / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsLi, D.Y. / Fan, S. / Jin, Y.Y. / Zhang, C. / Lv, G.X. / Wu, G.T. / Yang, Z.Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China81761128016 China
Other governmentCAMS Innovation Fund for Medical Sciences(2016-12M-3-012) China
Other governmentCAMS Innovation Fund for Medical Sciences(2016-12M-3-022) China
National Natural Science Foundation of China81621064 China
CitationJournal: Molecules / Year: 2021
Title: The Complex Structure of Protein AaLpxC from Aquifex aeolicus with ACHN-975 Molecule Suggests an Inhibitory Mechanism at Atomic-Level against Gram-Negative Bacteria
Authors: Fan, S. / Li, D. / Yan, M. / Feng, X. / Lv, G. / Wu, G. / Jin, Y. / Wang, Y. / Yang, Z.
History
DepositionSep 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Nov 22, 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)32,7424
Polymers32,0611
Non-polymers6813
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.569, 65.569, 131.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

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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: 32060.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: lpxC, envA, aq_1772
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O67648, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-A5F / N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide / ACHN-975


Mass: 369.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-A5U / methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate


Mass: 246.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H22N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 97208 / % possible obs: 99.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 14.36 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.02 / Net I/σ(I): 10
Reflection shellResolution: 1.21→1.25 Å / Num. unique obs: 2378 / CC1/2: 0.933 / Rpim(I) all: 0.136

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IER

2ier


Resolution: 1.21→50 Å / SU ML: 0.0772 / Cross valid method: FREE R-VALUE / Phase error: 16.7244
RfactorNum. reflection% reflection
Rfree0.1824 1970 2.17 %
Rwork0.1641 --
obs0.1645 90818 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.35 Å2
Refinement stepCycle: LAST / Resolution: 1.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 45 350 2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572247
X-RAY DIFFRACTIONf_angle_d1.03583029
X-RAY DIFFRACTIONf_chiral_restr0.091328
X-RAY DIFFRACTIONf_plane_restr0.0055385
X-RAY DIFFRACTIONf_dihedral_angle_d7.7401833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.240.19821220.18765682X-RAY DIFFRACTION83.88
1.24-1.280.20821330.18685929X-RAY DIFFRACTION87.93
1.28-1.310.19481410.18046175X-RAY DIFFRACTION90.84
1.31-1.360.15681380.17136260X-RAY DIFFRACTION93.37
1.36-1.40.17841430.16986358X-RAY DIFFRACTION94.05
1.4-1.460.19721350.1716182X-RAY DIFFRACTION91.04
1.46-1.530.15491410.16536437X-RAY DIFFRACTION95.37
1.53-1.610.17971440.15456506X-RAY DIFFRACTION96.22
1.61-1.710.16291520.15946531X-RAY DIFFRACTION96.98
1.71-1.840.17991440.16656607X-RAY DIFFRACTION97.45
1.84-2.020.17881410.16456318X-RAY DIFFRACTION93.34
2.02-2.320.17521460.15936692X-RAY DIFFRACTION98.45
2.32-2.920.20581430.17386726X-RAY DIFFRACTION99.08
2.92-26.070.181470.15676445X-RAY DIFFRACTION94.41

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