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- PDB-7k9a: Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide i... -

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Basic information

Entry
Database: PDB / ID: 7k9a
TitleCrystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor
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
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-W4P / Chem-W8P / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSacco, M. / Chen, Y.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay.
Authors: Furuya, T. / Shapiro, A.B. / Comita-Prevoir, J. / Kuenstner, E.J. / Zhang, J. / Ribe, S.D. / Chen, A. / Hines, D. / Moussa, S.H. / Carter, N.M. / Sylvester, M.A. / Romero, J.A.C. / Vega, C.V. ...Authors: Furuya, T. / Shapiro, A.B. / Comita-Prevoir, J. / Kuenstner, E.J. / Zhang, J. / Ribe, S.D. / Chen, A. / Hines, D. / Moussa, S.H. / Carter, N.M. / Sylvester, M.A. / Romero, J.A.C. / Vega, C.V. / Sacco, M.D. / Chen, Y. / O'Donnell, J.P. / Durand-Reville, T.F. / Miller, A.A. / Tommasi, R.A.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
C: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,10714
Polymers66,9502
Non-polymers2,15712
Water4,522251
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3617
Polymers33,4751
Non-polymers8866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7467
Polymers33,4751
Non-polymers1,2716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.621, 157.351, 48.846
Angle α, β, γ (deg.)90.000, 101.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#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: 33475.047 Da / Num. of mol.: 2
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 7 types, 263 molecules

#2: Chemical ChemComp-W4P / N-hydroxy-N-[(1S)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide


Mass: 462.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-W8P / N-hydroxy-N-[(1R)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide


Mass: 462.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N6O3S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M AmSO4, 0.5 M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34441 / % possible obs: 97.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.057 / Rrim(I) all: 0.13 / Χ2: 1.225 / Net I/σ(I): 5.2 / Num. measured all: 161786
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0340.43315900.8410.230.4930.55591.3
2.03-2.074.30.41716830.70.2210.4750.60895.2
2.07-2.114.20.36116950.8850.1870.4090.57795.5
2.11-2.154.30.36516870.890.1890.4140.57997.1
2.15-2.24.40.32717260.9170.1680.370.61897.6
2.2-2.254.50.3517220.7010.1830.3980.78997.9
2.25-2.314.50.29517380.9280.1530.3340.64698.7
2.31-2.374.60.26917490.9480.1370.3040.66498
2.37-2.444.20.25316790.9460.1350.2890.71295.7
2.44-2.5250.23317280.9620.1150.2610.6699.1
2.52-2.614.90.22417510.9660.110.250.76399.5
2.61-2.7150.20417610.9720.0990.2280.8299.2
2.71-2.8450.17817220.9760.0860.1990.85698.5
2.84-2.9950.14617600.9840.0710.1631.00398.6
2.99-3.174.60.11416830.990.0580.1291.13796.9
3.17-3.425.20.09717610.9910.0460.1081.38499.7
3.42-3.765.10.08317580.9930.040.0921.57999.4
3.76-4.315.10.07117460.990.0340.0792.0698.4
4.31-5.434.80.06217340.9940.030.0692.18997.1
5.43-5050.08517680.9840.040.0955.21498.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5u39

5u39


Resolution: 2→47.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.545 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1744 5.1 %RANDOM
Rwork0.1656 ---
obs0.1684 32662 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 31.885 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å21.2 Å2
2---2.06 Å2-0 Å2
3---3.13 Å2
Refinement stepCycle: final / Resolution: 2→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 139 260 5059
Biso mean--47.25 37.5 -
Num. residues----598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134929
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174633
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6686667
X-RAY DIFFRACTIONr_angle_other_deg1.2641.59510704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36721.969259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14415833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2571537
X-RAY DIFFRACTIONr_chiral_restr0.0640.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021063
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 130 -
Rwork0.218 2260 -
all-2390 -
obs--91.92 %

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