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- PDB-5u39: Pseudomonas aeruginosa LpxC in complex with CHIR-090 -

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Basic information

Entry
Database: PDB / ID: 5u39
TitlePseudomonas aeruginosa LpxC in complex with CHIR-090
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LPXC / HYDROXYMATE / GRAM NEGATIVE
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C90 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSprague, E.R.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design, Synthesis, and Properties of a Potent Inhibitor of Pseudomonas aeruginosa Deacetylase LpxC.
Authors: Piizzi, G. / Parker, D.T. / Peng, Y. / Dobler, M. / Patnaik, A. / Wattanasin, S. / Liu, E. / Lenoir, F. / Nunez, J. / Kerrigan, J. / McKenney, D. / Osborne, C. / Yu, D. / Lanieri, L. / ...Authors: Piizzi, G. / Parker, D.T. / Peng, Y. / Dobler, M. / Patnaik, A. / Wattanasin, S. / Liu, E. / Lenoir, F. / Nunez, J. / Kerrigan, J. / McKenney, D. / Osborne, C. / Yu, D. / Lanieri, L. / Bojkovic, J. / Dzink-Fox, J. / Lilly, M.D. / Sprague, E.R. / Lu, Y. / Wang, H. / Ranjitkar, S. / Xie, L. / Wang, B. / Glick, M. / Hamann, L.G. / Tommasi, R. / Yang, X. / Dean, C.R.
History
DepositionDec 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0173
Polymers32,5141
Non-polymers5032
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.230, 82.880, 87.530
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 UDP-3-O-acyl-N-acetylglucosamine deacetylase / / UDP-3-O-acyl-GlcNAc deacetylase / UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase


Mass: 32513.785 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: lpxC, envA, PA4406 / Production host: Escherichia coli (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C90 / N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide


Mass: 437.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.34M Tri-sodium citrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25668 / % possible obs: 96.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.01 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.017 / Net I/σ(I): 21.3 / Num. measured all: 131331
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.814.40.192178.2
1.81-1.895.10.146196.3
1.89-1.975.30.111196.7
1.97-2.075.30.076197.4
2.07-2.25.30.06198
2.2-2.385.30.05198.5
2.38-2.615.30.044198.9
2.61-2.995.20.039198.6
2.99-3.775.10.039199.3
3.77-504.80.03199.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P42

1p42


Resolution: 1.75→20.34 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9337 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.113 / Details: Initial refinement with CNX 2002
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 2493 9.87 %RANDOM
Rwork0.1731 ---
obs0.176 25269 94.99 %-
Displacement parametersBiso max: 93.28 Å2 / Biso mean: 23.19 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1-5.0091 Å20 Å20 Å2
2---3.9591 Å20 Å2
3----1.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: final / Resolution: 1.75→20.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 33 175 2447
Biso mean--23.82 31.07 -
Num. residues----287
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d847SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes351HARMONIC5
X-RAY DIFFRACTIONt_it2348HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion306SEMIHARMONIC5
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_contact3099SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2348HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3183HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion15.41
LS refinement shellResolution: 1.75→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2046 223 9.96 %
Rwork0.1889 2016 -
all0.1905 2239 -
obs--76.02 %
Refinement TLS params.Method: refined / Origin x: -4.1373 Å / Origin y: -3.1926 Å / Origin z: 9.7937 Å
111213212223313233
T0.0154 Å20.0139 Å2-0.0182 Å2-0.0153 Å2-0.0138 Å2--0.0262 Å2
L0.6701 °2-0.0872 °2-0.0306 °2-0.6675 °20.0356 °2--0.4894 °2
S0.0098 Å °-0.0184 Å °0.0315 Å °-0.0064 Å °-0.0056 Å °0.0017 Å °-0.008 Å °0.0069 Å °-0.0042 Å °
Refinement TLS groupSelection details: { A|* }

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