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- PDB-7t60: P. aeruginosa LpxA in complex with ligand L13 -

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Basic information

Entry
Database: PDB / ID: 7t60
TitleP. aeruginosa LpxA in complex with ligand L13
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / Lpxa / lipid A / LPS / lipopolysaccharide / UDP-N-acetylglucosamine O-acyltransferase
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-F9H / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSacco, M. / Chen, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis.
Authors: Sacco, M.D. / Defrees, K. / Zhang, X. / Lawless, W. / Nwanochie, E. / Balsizer, A. / Darch, S.E. / Renslo, A.R. / Chen, Y.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
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)172,72217
Polymers168,2926
Non-polymers4,43011
Water5,224290
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)86,51410
Polymers84,1463
Non-polymers2,3687
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-40 kcal/mol
Surface area28910 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)86,2087
Polymers84,1463
Non-polymers2,0624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-38 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.100, 82.220, 222.010
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 PA7 (bacteria) / Strain: PA7 / Gene: lpxA, PSPA7_1495
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-F9H / (3S)-3-(5,5-dimethyl-2-oxo-1,3-oxazolidin-3-yl)-N-(1H-tetrazol-5-yl)-1-[3-(trifluoromethyl)benzoyl]-2,3-dihydro-1H-indole-3-carboxamide


Mass: 515.445 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C23H20F3N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 1,000, 0.2 M CaOAc, 0.1 M imidazole pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→46.04 Å / Num. obs: 98941 / % possible obs: 99.2 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1 / % possible all: 97.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2-2.0370.8033321047200.7660.3180.8661.9
10.95-468.80.03862287110.9980.0130.0430

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ueg

6ueg


Resolution: 2→46.04 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.673 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 5004 5.1 %RANDOM
Rwork0.1919 ---
obs0.1933 93861 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.27 Å2 / Biso mean: 42.993 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å20 Å2
2--0.56 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11784 0 316 291 12391
Biso mean--53.31 43.65 -
Num. residues----1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312454
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711352
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.67616979
X-RAY DIFFRACTIONr_angle_other_deg1.291.59126129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69151549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94320.602664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.716151913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.16515109
X-RAY DIFFRACTIONr_chiral_restr0.2950.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022760
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 332 -
Rwork0.276 6789 -
all-7121 -
obs--97.82 %

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