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- PDB-6dui: Crystal structure of LpxC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6dui
TitleCrystal structure of LpxC from Pseudomonas aeruginosa in complex with PT801
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / SSGCID / LpxC / lipid A biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / hydrolase-hydrolase inhibitor complex
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-HAY / Chem-J1M / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PT801
Authors: Phan, J.N. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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)34,7287
Polymers33,5621
Non-polymers1,1666
Water7,404411
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)35.710, 48.000, 48.130
Angle α, β, γ (deg.)111.32, 108.56, 98.83
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#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: 33562.125 Da / Num. of mol.: 1 / Fragment: PsaeA.00166.a.DG15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain LESB58) (bacteria)
Strain: LESB58 / Gene: lpxC, PLES_47851 / Plasmid: PsaeA.00166.a.DG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 6 types, 417 molecules

#2: Chemical ChemComp-HAY / (2R)-4-{4-[4-(benzyloxy)phenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 470.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N2O6S
#3: Chemical ChemComp-J1M / (2S)-4-{4-[4-(benzyloxy)phenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 470.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N2O6S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES HCl, pH 7.5, 50mM CaCl2, 4% (w/v) Propanol, 25% (w/v) PEG 3350, PsaeA.00166.a.DG15.PD00442 at 5mg/ml + 1mM ZnCl2 + 1mM BSI 108451, Cryo = 20%EG: tray 298107e10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 8, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→42.585 Å / Num. obs: 37740 / % possible obs: 96.4 % / Redundancy: 3.952 % / Biso Wilson estimate: 12.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.089 / Χ2: 1.008 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.593.9860.5072.6926940.8440.58694.4
1.59-1.633.990.4213.2626780.8890.48794.9
1.63-1.683.9840.3733.5926140.9070.43195
1.68-1.733.9870.3064.2925460.9330.35395.1
1.73-1.793.9770.2495.3224850.9520.28895.8
1.79-1.853.9740.2146.1524090.9630.24895.9
1.85-1.923.970.1647.7723010.9770.1996.3
1.92-23.9680.1329.6322470.9840.15396.2
2-2.093.9540.10811.4521490.9880.12596.5
2.09-2.193.9590.09312.7320430.9920.10896.9
2.19-2.313.9440.08214.4219670.9910.09597
2.31-2.453.9310.07415.8218640.9940.08597.8
2.45-2.623.9250.06916.9817520.9930.0897.5
2.62-2.833.9220.05918.8416640.9950.06897.5
2.83-3.13.8970.05420.514740.9960.06398
3.1-3.473.8910.04823.2514000.9960.05698.1
3.47-43.8720.04425.1812130.9970.05198
4-4.93.8810.0426.6510160.9970.04799
4.9-6.933.9030.04426.367960.9980.05197.8
6.93-42.5853.8220.04127.084280.9980.04797.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UPG

5upg


Resolution: 1.55→42.585 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 2034 5.39 %
Rwork0.1496 --
obs0.1517 37735 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→42.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 76 411 2818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062597
X-RAY DIFFRACTIONf_angle_d0.8383550
X-RAY DIFFRACTIONf_dihedral_angle_d19.311592
X-RAY DIFFRACTIONf_chiral_restr0.056405
X-RAY DIFFRACTIONf_plane_restr0.005458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5499-1.5860.25061310.2152292X-RAY DIFFRACTION95
1.586-1.62560.22571510.20232324X-RAY DIFFRACTION95
1.6256-1.66960.28031270.19912341X-RAY DIFFRACTION96
1.6696-1.71870.22811470.18842367X-RAY DIFFRACTION96
1.7187-1.77420.21541180.17982375X-RAY DIFFRACTION96
1.7742-1.83760.23271390.18212339X-RAY DIFFRACTION96
1.8376-1.91120.21961170.17012399X-RAY DIFFRACTION96
1.9112-1.99810.22541250.15342403X-RAY DIFFRACTION97
1.9981-2.10350.16541200.14722409X-RAY DIFFRACTION97
2.1035-2.23530.1951470.14692353X-RAY DIFFRACTION97
2.2353-2.40780.19371440.15452429X-RAY DIFFRACTION98
2.4078-2.65010.19181380.15712393X-RAY DIFFRACTION98
2.6501-3.03350.1791530.14852408X-RAY DIFFRACTION98
3.0335-3.82150.16141580.12082401X-RAY DIFFRACTION99
3.8215-42.60140.14821190.12052468X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6508-1.2170.33424.41362.23192.7740.05140.1104-0.0875-0.2694-0.21660.3482-0.1709-0.17890.17160.0534-0.02440.0430.09670.04490.0539-7.57662.9064-10.4881
20.66780.42650.03171.14420.55190.4569-0.02850.1790.1621-0.1478-0.0084-0.0543-0.0915-0.05540.02940.13890.0192-0.00790.120.05160.112-2.21999.5756-14.3136
33.79380.0948-0.51794.3756-1.20554.54540.0211-0.06270.21340.14720.0064-0.1159-0.270.2296-0.02610.0859-0.0105-0.00170.08230.02360.09926.89949.8284-4.1194
40.8395-0.0351-0.21121.69630.65390.39710.01980.06050.0686-0.0529-0.03960.0175-0.0274-0.06980.01710.10020.0129-0.00770.11110.020.0724-6.96013.537-6.0234
52.7463-0.44920.97921.49020.51133.10430.12060.0022-0.12030.08260.0468-0.12670.19510.2519-0.17390.0628-0.0240.03180.04140.02780.08136.9312-9.3071-2.715
61.138-2.5239-2.89255.60976.36978.1630.0165-0.0946-0.04370.3719-0.0414-0.00550.3296-0.11190.03490.1517-0.0312-0.00990.14730.01510.08380.1121-5.670314.8149
70.97020.1282-0.03811.7060.76982.05540.0389-0.11810.05430.1119-0.10010.1318-0.0688-0.0840.06310.09110.0028-0.0030.11320.00250.0647-5.80474.020610.0194
82.47330.49250.072.40181.42351.84320.0363-0.0034-0.02530.0375-0.0004-0.10990.06990.0455-0.03080.06680.0202-0.0180.07490.0310.072210.6595-6.67280.2623
97.07613.66341.54473.2903-0.29764.2138-0.0407-0.0253-0.0484-0.07320.1401-0.27820.2348-0.1102-0.07640.1081-0.0062-0.01270.11220.0030.0826-4.4822-18.1816-11.0168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 147 )
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 170 )
7X-RAY DIFFRACTION7chain 'A' and (resid 171 through 249 )
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 299 )

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