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- PDB-6ueg: Pseudomonas aeruginosa LpxA Complex Structure with Ligand -

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Basic information

Entry
Database: PDB / ID: 6ueg
TitlePseudomonas aeruginosa LpxA Complex Structure with Ligand
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / LpxA / Ligand Complex / Trimer / Acyl Transferase
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; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-Q5G / 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
AuthorsChen, Y. / Kroeck, K. / Sacco, M.
CitationJournal: Sci Rep / Year: 2019
Title: Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography.
Authors: Kroeck, K.G. / Sacco, M.D. / Smith, E.W. / Zhang, X. / Shoun, D. / Akhtar, A. / Darch, S.E. / Cohen, F. / Andrews, L.D. / Knox, J.E. / Chen, Y.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 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
D: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,27913
Polymers168,2926
Non-polymers1,9867
Water13,908772
1
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)85,1597
Polymers84,1463
Non-polymers1,0134
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-43 kcal/mol
Surface area28850 Å2
MethodPISA
2
D: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1196
Polymers84,1463
Non-polymers9733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-43 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.390, 82.520, 224.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28048.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria)
Strain: PA7 / Gene: lpxA, PSPA7_1495 / Production host: Escherichia coli (E. coli)
References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical
ChemComp-Q5G / 3-({2-[(2R)-2-carbamoyl-2,3-dihydro-4H-1,4-benzoxazin-4-yl]-2-oxoethyl}sulfanyl)propanoic acid


Mass: 324.352 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H16N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 1000 0.2M calcium acetate 0.1M imidazole pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→111.725 Å / Num. obs: 79561 / % possible obs: 87.6 % / Redundancy: 5.1 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.102 / Rsym value: 0.092 / Net I/av σ(I): 7.1 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.2-2.325.30.4541.782700.2010.4990.45476
2.32-2.465.10.374280380.1670.4110.37477.8
2.46-2.634.90.2872.678490.130.3170.28780.8
2.63-2.844.60.2013.877500.0920.2230.20185.3
2.84-3.114.50.125676180.0590.1390.12590.7
3.11-3.484.60.0878.273290.0420.0970.08796.1
3.48-4.0250.0659.866860.0310.0730.06598.8
4.02-4.925.60.04712.757740.0210.0520.04799.8
4.92-6.966.50.04513.945530.0190.0480.04599.9
2-2.0726.80.0412.726510.0160.0430.0499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→55.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.272 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 4307 5.1 %RANDOM
Rwork0.1762 ---
obs0.1792 79561 82.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.78 Å2 / Biso mean: 23.616 Å2 / Biso min: 1.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 2→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11753 0 133 792 12678
Biso mean--40.26 30.62 -
Num. residues----1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01312209
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711116
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.65116587
X-RAY DIFFRACTIONr_angle_other_deg1.2421.57325617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6451547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45220.7657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.261151895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3615106
X-RAY DIFFRACTIONr_chiral_restr0.0650.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022661
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 295 -
Rwork0.271 5336 -
all-5631 -
obs--76.03 %

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