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- PDB-8e4a: Pseudomonas LpxC in complex with LPC-233 -

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Basic information

Entry
Database: PDB / ID: 8e4a
TitlePseudomonas LpxC in complex with LPC-233
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsBIOSYNTHETIC PROTEIN / LpxC / lipid A
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 / membrane
Similarity search - Function
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-type fold
Similarity search - Domain/homology
Chem-UFX / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.034 Å
AuthorsNajeeb, J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Transl Med / Year: 2023
Title: Preclinical safety and efficacy characterization of an LpxC inhibitor against Gram-negative pathogens.
Authors: Zhao, J. / Cochrane, C.S. / Najeeb, J. / Gooden, D. / Sciandra, C. / Fan, P. / Lemaitre, N. / Newns, K. / Nicholas, R.A. / Guan, Z. / Thaden, J.T. / Fowler Jr., V.G. / Spasojevic, I. / ...Authors: Zhao, J. / Cochrane, C.S. / Najeeb, J. / Gooden, D. / Sciandra, C. / Fan, P. / Lemaitre, N. / Newns, K. / Nicholas, R.A. / Guan, Z. / Thaden, J.T. / Fowler Jr., V.G. / Spasojevic, I. / Sebbane, F. / Toone, E.J. / Duncan, C. / Gammans, R. / Zhou, P.
History
DepositionAug 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5883
Polymers33,1471
Non-polymers4422
Water4,882271
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)35.970, 66.450, 63.840
Angle α, β, γ (deg.)90.000, 90.676, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxC / Production host: Escherichia coli (E. coli)
References: UniProt: A0A072ZC86, 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-UFX / 4-(4-cyclopropylbuta-1,3-diyn-1-yl)-N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]benzamide


Mass: 376.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18F2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 mM protein, 0.6 mM LPC-233, 12.5 mM HEPES (pH 7.1), 25 mM NaCl, 1 mM TCEP, 0.085 M sodium acetate, 0.0425 M Tris HCl pH 8.5, 12.75% PEG 4000, 7.5% glycerol, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.034→46.04 Å / Num. obs: 17695 / % possible obs: 91.08 % / Redundancy: 2.7 % / Biso Wilson estimate: 15.07 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1042 / Net I/σ(I): 10.21
Reflection shellResolution: 2.034→2.107 Å / Num. unique obs: 1801 / CC1/2: 0.808 / CC star: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3E

3p3e


Resolution: 2.034→46.04 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.0137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 885 5 %
Rwork0.1716 16807 -
obs0.1733 17692 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.19 Å2
Refinement stepCycle: LAST / Resolution: 2.034→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 28 271 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192420
X-RAY DIFFRACTIONf_angle_d0.50313286
X-RAY DIFFRACTIONf_chiral_restr0.044375
X-RAY DIFFRACTIONf_plane_restr0.0039431
X-RAY DIFFRACTIONf_dihedral_angle_d8.7001341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.034-2.160.2721480.22072823X-RAY DIFFRACTION92.7
2.16-2.330.23891490.19192823X-RAY DIFFRACTION92.41
2.33-2.560.2331490.19012829X-RAY DIFFRACTION91.74
2.56-2.930.22621480.17932812X-RAY DIFFRACTION91.93
2.93-3.70.18151470.15552794X-RAY DIFFRACTION90.72
3.7-46.040.15881440.14462726X-RAY DIFFRACTION87.13
Refinement TLS params.Method: refined / Origin x: 10.0592583112 Å / Origin y: 4.85985865418 Å / Origin z: 76.3989130805 Å
111213212223313233
T0.050673194027 Å20.00433212947781 Å20.00429537345348 Å2-0.0488514153225 Å20.00214661856523 Å2--0.0493107943458 Å2
L0.236379696975 °20.0175293738903 °20.146991978628 °2-0.146745945363 °20.0149554553928 °2--0.0961943862451 °2
S0.0185151309318 Å °0.00408000873059 Å °0.00505963096765 Å °0.00664697168906 Å °-0.00392328440599 Å °0.021852819657 Å °-0.014470334431 Å °0.0028413771179 Å °0.000372850353041 Å °
Refinement TLS groupSelection details: all

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