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- PDB-6mae: CHAIN A. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacety... -

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Basic information

Entry
Database: PDB / ID: 6mae
TitleCHAIN A. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase PA-LPXC Complexed with (R)-3-((S)-3-(4-(cyclopropylethynyl)phenyl)-2-oxooxazolidin-5-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)propenamide
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LPXC
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-JBA / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsShu, W.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Application of Virtual Screening to the Identification of New LpxC Inhibitor Chemotypes, Oxazolidinone and Isoxazoline.
Authors: Lee, P.S. / Lapointe, G. / Madera, A.M. / Simmons, R.L. / Xu, W. / Yifru, A. / Tjandra, M. / Karur, S. / Rico, A. / Thompson, K. / Bojkovic, J. / Xie, L. / Uehara, K. / Liu, A. / Shu, W. / ...Authors: Lee, P.S. / Lapointe, G. / Madera, A.M. / Simmons, R.L. / Xu, W. / Yifru, A. / Tjandra, M. / Karur, S. / Rico, A. / Thompson, K. / Bojkovic, J. / Xie, L. / Uehara, K. / Liu, A. / Shu, W. / Bellamacina, C. / McKenney, D. / Morris, L. / Tonn, G.R. / Osborne, C. / Benton, B.M. / McDowell, L. / Fu, J. / Sweeney, Z.K.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 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: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6353
Polymers33,1631
Non-polymers4722
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.002, 67.346, 62.864
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211

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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: 33162.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) 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
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-JBA / (2R)-3-{(5S)-3-[4-(cyclopropylethynyl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)propanamide


Mass: 406.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O6S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES PH 6.5, 20% PEG4000, 0.6M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→67.35 Å / Num. obs: 27108 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.983.80.50363850.7960.3010.58797.1
4.42-67.353.60.03419280.9980.0210.0498.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREPphasing
BUSTER2.11.4refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→62.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9416 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 1364 5.04 %RANDOM
Rwork0.1593 ---
obs0.1614 27085 97.13 %-
Displacement parametersBiso max: 96.47 Å2 / Biso mean: 21.67 Å2 / Biso min: 4.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.6852 Å20 Å20.1178 Å2
2--0.1728 Å20 Å2
3----0.8581 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: final / Resolution: 1.8→62.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 51 333 2685
Biso mean--17.21 35.36 -
Num. residues----297
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d855SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes368HARMONIC5
X-RAY DIFFRACTIONt_it2409HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3044SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2409HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3285HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion15.6
LS refinement shellResolution: 1.8→1.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2322 143 5.32 %
Rwork0.21 2544 -
all0.2113 2687 -
obs--97.13 %
Refinement TLS params.Method: refined / Origin x: 10.9274 Å / Origin y: 0.8353 Å / Origin z: 12.7267 Å
111213212223313233
T-0.0239 Å20.0056 Å20.011 Å2--0.0307 Å20.0078 Å2---0.0313 Å2
L0.6054 °2-0.0378 °20.1432 °2-0.4363 °20.0897 °2--0.368 °2
S0.0626 Å °0.0409 Å °0.0494 Å °0.0361 Å °-0.0207 Å °0.0007 Å °-0.0122 Å °0.013 Å °-0.0418 Å °
Refinement TLS groupSelection details: { A|* }

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