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- PDB-7okc: Crystal structure of Escherichia coli LpxA in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 7okc
TitleCrystal structure of Escherichia coli LpxA in complex with compound 1
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-VFE / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8523
Polymers28,3991
Non-polymers4532
Water3,351186
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)86,5579
Polymers85,1983
Non-polymers1,3596
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area6690 Å2
ΔGint-59 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.086, 96.086, 96.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1260-

HOH

21A-1285-

HOH

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Components

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


Mass: 28399.287 Da / Num. of mol.: 1 / Fragment: full-length protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: C3TPH2, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-VFE / 2-[2-(2-chlorophenyl)sulfanylethanoyl-[[4-(1,2,4-triazol-1-yl)phenyl]methyl]amino]-N-methyl-ethanamide


Mass: 429.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20ClN5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.63 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 1.8 M NaH2PO4 / Na2HPO4 pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→67.94 Å / Num. obs: 25927 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 20.218 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.058 / Rrim(I) all: 0.256 / Net I/σ(I): 8.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 18.2 % / Rmerge(I) obs: 2.704 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1274 / CC1/2: 0.687 / Rpim(I) all: 0.65 / Rrim(I) all: 2.782 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JF3

2jf3


Resolution: 1.84→67.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.887 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 1267 4.9 %RANDOM
Rwork0.1734 ---
obs0.1755 24607 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.72 Å2 / Biso mean: 27.521 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.84→67.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1991 0 30 186 2207
Biso mean--31.53 34.45 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142063
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171855
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6672795
X-RAY DIFFRACTIONr_angle_other_deg0.9751.6484331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48121.524105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6661515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02391
LS refinement shellResolution: 1.841→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 77 -
Rwork0.256 1805 -
all-1882 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 27.0088 Å / Origin y: -3.945 Å / Origin z: -5.2556 Å
111213212223313233
T0.0201 Å2-0.0098 Å20.0052 Å2-0.0369 Å2-0.0061 Å2--0.0199 Å2
L1.9129 °2-0.1843 °20.8533 °2-0.5772 °2-0.0874 °2--1.451 °2
S0.0089 Å °-0.0247 Å °0.0027 Å °-0.025 Å °-0.0106 Å °0.0928 Å °0.019 Å °-0.1994 Å °0.0016 Å °

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