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- PDB-7ojy: Crystal structure of Pseudomonas aeruginosa LpxA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ojy
TitleCrystal structure of Pseudomonas aeruginosa LpxA in complex with compound 6
ComponentsAcyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / ACYLTRANSFERASE / FATTY ACIDS / LIPID A / LEFT-HANDED PARALLEL BETA-HELIX
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / cytoplasm
Similarity search - Function
UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Chem-VGQ / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRyan, M.D. / Parkes, A.L. / Southey, M. / Andersen, O.A. / Zahn, M. / Barker, J. / DeJonge, B.L.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Novel UDP- N -Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa .
Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, ...Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, M. / Dorali, A. / Etheridge, D. / Evans, S. / Faulkner, A. / Gadouleau, E. / Gorman, T. / Haase, D. / Holbrow-Wilshaw, M. / Krulle, T. / Li, X. / Lumley, C. / Mertins, B. / Napier, S. / Odedra, R. / Papadopoulos, K. / Roumpelakis, V. / Spear, K. / Trimby, E. / Williams, J. / Zahn, M. / Keefe, A.D. / Zhang, Y. / Soutter, H.T. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Deng, B. / Hunt, A. / Sigel, E.A. / Troast, D.M. / DeJonge, B.L.M.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection
Category: database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Revision 1.2Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,73420
Polymers84,9933
Non-polymers1,74117
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-186 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.392, 166.392, 99.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 28331.010 Da / Num. of mol.: 3 / Fragment: full-length protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Strain: PA7 / Gene: lpxA, PSPA7_1495 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-VGQ / 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-[(5-oxidanyl-1,3,4-oxadiazol-2-yl)methyl]ethanamide


Mass: 414.865 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H15ClN4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5 M NH4Cl, 0.1 M Na Acetate pH 4.5

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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 EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→83.2 Å / Num. obs: 91413 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.067 / Rrim(I) all: 0.175 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.036.91.35642240.6650.5571.46793.4
5.42-83.276.60.06847100.9790.0290.074100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEM

5dem


Resolution: 2→58.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4470 4.9 %RANDOM
Rwork0.193 ---
obs0.195 91289 99.5 %-
Displacement parametersBiso max: 133.03 Å2 / Biso mean: 48.35 Å2 / Biso min: 26.29 Å2
Baniso -1Baniso -2Baniso -3
1-8.2308 Å20 Å20 Å2
2--8.2308 Å20 Å2
3----16.4617 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2→58.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 98 516 6536
Biso mean--39.96 51.13 -
Num. residues----774
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2067SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1086HARMONIC5
X-RAY DIFFRACTIONt_it6138HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion804SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7662SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6138HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8328HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion15.63
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2521 109 5.97 %
Rwork0.2029 1717 -
all0.2056 1826 -
obs--83.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0779-0.38110.22571.06940.07790.84820.03710.09160.372-0.0861-0.0213-0.0071-0.1081-0.0377-0.0158-0.0836-0.01080.0354-0.1179-0.05920.01311.30358.9699-19.7126
22.17640.04690.8241.18320.01191.10290.0092-0.1935-0.0180.00420.0030.25140.0717-0.2371-0.0121-0.112-0.03250.0292-0.0684-0.0562-0.0406-13.249831.6652-16.9149
32.2363-0.68650.35841.8133-0.37771.05360.02270.38430.0719-0.4696-0.08770.00350.0311-0.06270.065-0.0313-0.02280.0451-0.113-0.0523-0.14056.687836.4802-40.2508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 258
2X-RAY DIFFRACTION2{ B|* }B1 - 258
3X-RAY DIFFRACTION3{ C|* }C1 - 258

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