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- PDB-6uec: Pseudomonas aeruginosa LpxD Complex Structure with Ligand -

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Basic information

Entry
Database: PDB / ID: 6uec
TitlePseudomonas aeruginosa LpxD Complex Structure with Ligand
ComponentsUDP-3-O-acylglucosamine N-acyltransferase
KeywordsTRANSFERASE / LpxD / Ligand Complex / Trimer / Acyl Transferase
Function / homology
Function and homology information


UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process
Similarity search - Function
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat ...UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region / UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD / MurE/MurF, N-terminal domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-(naphthalen-1-yl)-4-oxobutanoic acid / UDP-3-O-acylglucosamine N-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4244
Polymers38,0931
Non-polymers3313
Water45025
1
A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules

A: UDP-3-O-acylglucosamine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,27112
Polymers114,2793
Non-polymers9929
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16430 Å2
ΔGint-126 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.764, 104.764, 95.967
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-403-

MG

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Components

#1: Protein UDP-3-O-acylglucosamine N-acyltransferase


Mass: 38092.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lpxD, PA3646 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HXY6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-Q5M / 4-(naphthalen-1-yl)-4-oxobutanoic acid


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350 0.2M Magnesium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→32.99 Å / Num. obs: 12038 / % possible obs: 99.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 3.4
Reflection shellResolution: 2.601→2.693 Å / Num. unique obs: 1223 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→32.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.873 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.63 / ESU R Free: 0.349
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 583 4.8 %RANDOM
Rwork0.2089 ---
obs0.2128 11529 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.87 Å2 / Biso mean: 52.423 Å2 / Biso min: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.33 Å20 Å2
2---0.67 Å20 Å2
3---2.16 Å2
Refinement stepCycle: final / Resolution: 2.6→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 22 25 2418
Biso mean--53.77 40.05 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172247
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.633306
X-RAY DIFFRACTIONr_angle_other_deg1.2681.5695165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6695336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14522.32399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.11815349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1281513
X-RAY DIFFRACTIONr_chiral_restr0.0580.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
LS refinement shellResolution: 2.6→2.663 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.382 36 -
Rwork0.288 855 -
obs--97.91 %

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