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- PDB-4u3d: LpxC from A.Aaeolicus in complex with 4-[[4-[2-[4-(morpholinometh... -

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Basic information

Entry
Database: PDB / ID: 4u3d
TitleLpxC from A.Aaeolicus in complex with 4-[[4-[2-[4-(morpholinomethyl)phenyl]ethynyl]phenoxy]methyl]tetrahydropyran-4-carbohydroxamic acid (compound 9)
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / antibacterial / lpxc / gram negative bacteria / MMP / hydrophobe
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / : / 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-3BX / IMIDAZOLE / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOlivier, N.B.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors.
Authors: Murphy-Benenato, K.E. / Olivier, N. / Choy, A. / Ross, P.L. / Miller, M.D. / Thresher, J. / Gao, N. / Hale, M.R.
History
DepositionJul 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6756
Polymers30,9901
Non-polymers6865
Water6,792377
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-42 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.865, 65.865, 133.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 30989.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: lpxC, envA, aq_1772 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 382 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-3BX / N-hydroxy-4-[(4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}phenoxy)methyl]tetrahydro-2H-pyran-4-carboxamide


Mass: 450.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30N2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Protein solution: 25 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 0.1 mM ZnSO4, 5% glycerol, 1 mM inhibitor. Well solution: 15% PEG 550 MME, 15% PEG 20K, 50 mM Imidazole and 50 mM MES (Morpheus buffer ...Details: Protein solution: 25 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 0.1 mM ZnSO4, 5% glycerol, 1 mM inhibitor. Well solution: 15% PEG 550 MME, 15% PEG 20K, 50 mM Imidazole and 50 mM MES (Morpheus buffer 1), pH 6.5, 2% 1,6-Hexanediol; 2% 1-Butanol 1,2-Propanediol (racemic); 2% 2-Propanol; 2% 1,4-Butanediol; 2% 1,3-Propanediol
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2012 / Details: monochromator
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.246→133.282 Å / Num. all: 89070 / Num. obs: 89070 / % possible obs: 97.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 12.26 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.08 / Rsym value: 0.071 / Net I/av σ(I): 5.763 / Net I/σ(I): 20.9 / Num. measured all: 958795
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.25-1.3110.80.5371.3137480127360.1760.5374.395.8
1.31-1.3910.80.3891.8130346121130.1280.3896.296.5
1.39-1.4911.10.2422.9127073114510.0790.2429.897.1
1.49-1.6110.80.1644.3116024107520.0550.16414.797.7
1.61-1.76110.118610933599030.0390.11820.998.3
1.76-1.9710.70.0887.99727190620.030.0882998.8
1.97-2.2710.60.079.78551380330.0240.0737.799.2
2.27-2.7910.30.06110.97001667900.0210.06142.599.6
2.79-3.9410.40.05211.45491752880.0180.05247.399.9
3.94-133.28210.50.04213.73082029420.0140.04250100

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
XDSdata reduction
PDB_EXTRACT3.14data extraction
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GO4

2go4


Resolution: 1.25→35.05 Å / Cor.coef. Fo:Fc: 0.9677 / Cor.coef. Fo:Fc free: 0.9646 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.038 / SU Rfree Blow DPI: 0.038 / SU Rfree Cruickshank DPI: 0.037
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 4427 5.02 %RANDOM
Rwork0.1575 ---
obs0.1581 88205 97.87 %-
Displacement parametersBiso max: 122.8 Å2 / Biso mean: 18.21 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.2485 Å20 Å20 Å2
2--1.2485 Å20 Å2
3----2.4969 Å2
Refine analyzeLuzzati coordinate error obs: 0.121 Å
Refinement stepCycle: final / Resolution: 1.25→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 41 377 2559
Biso mean--18.94 34.84 -
Num. residues----267
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d849SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2323HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion289SEMIHARMONIC5
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_contact3102SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2323HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3147HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.66
X-RAY DIFFRACTIONt_other_torsion14.87
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2009 319 5 %
Rwork0.1831 6066 -
all0.184 6385 -
obs--97.87 %

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