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- PDB-7ok1: Crystal structure of Pseudomonas aeruginosa LpxA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7ok1
TitleCrystal structure of Pseudomonas aeruginosa LpxA in complex with compound 3
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 / membrane / 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-VFN / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Jan 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)86,44712
Polymers84,9933
Non-polymers1,4549
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-95 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.046, 166.046, 98.540
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)
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-VFN / ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide


Mass: 413.881 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16ClN5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 344 / 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 EIGER2 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: 1.92→84.741 Å / Num. obs: 62977 / % possible obs: 86.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.046 / Rrim(I) all: 0.121 / Net I/σ(I): 10.6
Reflection shellResolution: 1.92→2.12 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.132 / Num. unique obs: 3153 / CC1/2: 0.622 / Rpim(I) all: 0.479 / Rrim(I) all: 1.232 / % possible all: 35.7

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Processing

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

5dem


Resolution: 1.92→27.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3229 5.13 %RANDOM
Rwork0.191 ---
obs0.193 62939 62 %-
Displacement parametersBiso max: 126.49 Å2 / Biso mean: 44.08 Å2 / Biso min: 17 Å2
Baniso -1Baniso -2Baniso -3
1--1.7124 Å20 Å20 Å2
2---1.7124 Å20 Å2
3---3.4247 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.92→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 90 344 6272
Biso mean--34.01 43.09 -
Num. residues----765
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2042SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1084HARMONIC5
X-RAY DIFFRACTIONt_it6069HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion799SEMIHARMONIC5
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_contact7447SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6069HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8241HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.22
LS refinement shellResolution: 1.92→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2516 55 4.37 %
Rwork0.1919 1204 -
all0.1944 1259 -
obs--8.06 %
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)
11.33210.5830.12992.1684-0.3340.8976-0.01910.0687-0.0439-0.02810.0369-0.3318-0.04560.1181-0.0178-0.14440.0142-0.0494-0.1145-0.05550.071-24.4426-1.220329.6672
21.32870.0078-0.15142.5651-1.12211.4025-0.0194-0.04030.22570.2426-0.01160.0173-0.2854-0.07910.0309-0.11560.0384-0.0509-0.1487-0.04290.0037-51.654813.311532.1732
31.84490.5886-0.40872.3151-0.52791.2753-0.08170.45080.0292-0.32590.0127-0.0676-0.0707-0.02780.0691-0.16990.0144-0.0408-0.0746-0.0584-0.0574-46.2535-6.74249.2544
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|* }C2 - 258

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