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- PDB-4u3b: LpxC from A.Aaeolicus in complex with the MMP inhibitor 4-[[4-(4-... -

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Basic information

Entry
Database: PDB / ID: 4u3b
TitleLpxC from A.Aaeolicus in complex with the MMP inhibitor 4-[[4-(4-chlorophenoxy)phenyl]sulfanylmethyl]tetrahydropyran-4-carbohydroxamic acid - compound 2
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-3BW / IMIDAZOLE / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 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 1.2Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3May 8, 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

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)31,6547
Polymers30,9901
Non-polymers6656
Water6,017334
1


  • Idetical with deposited unit
  • defined by software
  • MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-51 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.929, 65.929, 133.556
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, 340 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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-3BW / 4-({[4-(4-chlorophenoxy)phenyl]sulfanyl}methyl)-N-hydroxytetrahydro-2H-pyran-4-carboxamide


Mass: 393.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClNO4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Protein buffer: 25 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 0.1 mM ZnSO4, 5% glycerol. 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- ...Details: Protein buffer: 25 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 0.1 mM ZnSO4, 5% glycerol. 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: 6.4 - 7.5

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Data collection

DiffractionMean temperature: 110 K / Ambient temp details: nitrogen gas stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 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: 1.34→133 Å / Num. all: 71559 / Num. obs: 71559 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 16.05 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.5
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.44 / % possible all: 89.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
BUSTER2.11.2refinement
XSCALEdata reduction
RefinementResolution: 1.34→26.8 Å / Cor.coef. Fo:Fc: 0.9629 / Cor.coef. Fo:Fc free: 0.9538 / SU R Cruickshank DPI: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.046 / SU Rfree Blow DPI: 0.048 / SU Rfree Cruickshank DPI: 0.047
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 3599 5.03 %RANDOM
Rwork0.1629 ---
obs0.164 71490 97.3 %-
Displacement parametersBiso max: 92.25 Å2 / Biso mean: 21.53 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.3654 Å20 Å20 Å2
2--2.3654 Å20 Å2
3----4.7307 Å2
Refine analyzeLuzzati coordinate error obs: 0.147 Å
Refinement stepCycle: final / Resolution: 1.34→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 35 334 2507
Biso mean--20.37 35.44 -
Num. residues----267
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d790SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes330HARMONIC5
X-RAY DIFFRACTIONt_it2224HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2900SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2224HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2997HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.66
X-RAY DIFFRACTIONt_other_torsion15.2
LS refinement shellResolution: 1.34→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2208 193 4.87 %
Rwork0.1963 3774 -
all0.1975 3967 -
obs--97.3 %
Refinement TLS params.Method: refined / Origin x: -2.9504 Å / Origin y: 29.7967 Å / Origin z: 0.0017 Å
111213212223313233
T-0.034 Å2-0.0016 Å20.0028 Å2--0.034 Å2-0.0031 Å2---0.0248 Å2
L0.7414 °20.0429 °2-0.2781 °2-0.5712 °20.2973 °2--0.5965 °2
S-0.006 Å °-0.0352 Å °-0.0254 Å °0.0339 Å °-0.0088 Å °-0.0046 Å °0.0356 Å °0.0409 Å °0.0147 Å °
Refinement TLS groupSelection details: { A|* }

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