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- PDB-5vwm: Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosa... -

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Basic information

Entry
Database: PDB / ID: 5vwm
TitleCrystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHydrolase/Hydrolase Inhibitor / inhibitor / Seattle Structural Genomics Center for Infectious Disease / SSGCID / LpxC / Hydrolase-Hydrolase Inhibitor complex
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
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-C90 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor
Authors: Delker, S.L. / Mayclin, S.J. / Phan, J.N. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionMay 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source
Revision 1.3Feb 6, 2019Group: Data collection / Other / Category: pdbx_SG_project
Revision 1.4Oct 4, 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)45,4618
Polymers44,6971
Non-polymers7657
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.850, 47.590, 48.410
Angle α, β, γ (deg.)111.300, 109.000, 98.390
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: 44696.633 Da / Num. of mol.: 1
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 / Plasmid: PsaeA.00166.a.DG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 6 types, 366 molecules

#2: Chemical ChemComp-C90 / N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide


Mass: 437.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N3O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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

Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: tray289953 G9:HEPES, 100 mM HCl, pH 7.7, 50 mM CaCl, 4% (w/v) Propanol, 25% (w/v) PEG 3350 +1mM ZnCl2, 1mM Chir-090 : Cryo = 20%EG : PsaeA.00166.a.DG15.PD00471 at 5 mg/ml, puck SHD-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97872 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 2017 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→42.297 Å / Num. obs: 23497 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 4.035 % / Biso Wilson estimate: 10.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.059 / Χ2: 0.991 / Net I/σ(I): 18.56 / Num. measured all: 94804 / Scaling rejects: 203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.7340.1825.0215290.950.22583.3
1.85-1.92.7490.156.1315130.9710.18583.7
1.9-1.952.7670.1247.6715280.9760.15388.3
1.95-2.012.7780.1068.9215520.9810.13190
2.01-2.082.8310.08910.8515280.9870.1192.7
2.08-2.153.1230.08312.4915170.9890.195.4
2.15-2.233.5860.07614.214920.9930.0995.6
2.23-2.323.7990.07515.5814310.9930.08897.5
2.32-2.433.9780.06817.1213890.9940.07996.3
2.43-2.554.2010.06717.8613380.9940.07797.6
2.55-2.684.5960.06419.6312550.9960.07397.7
2.68-2.855.3010.06122.6111880.9970.06898
2.85-3.045.6460.05525.9611260.9980.0697.3
3.04-3.295.6320.04830.610520.9980.05397.9
3.29-3.65.5870.04334.249730.9990.04798.2
3.6-4.035.6080.03838.538680.9990.04298.2
4.03-4.655.5850.03441.677780.9990.03799
4.65-5.695.5920.03238.246540.9990.03699.5
5.69-8.055.5190.04234.115130.9980.04697.9
8.05-42.2975.2890.03144.732730.9990.03596.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2733refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3uhm

3uhm


Resolution: 1.8→42.297 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.98
RfactorNum. reflection% reflection
Rfree0.1785 2033 8.66 %
Rwork0.1382 --
obs0.1418 23488 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.45 Å2 / Biso mean: 13.4029 Å2 / Biso min: 3.07 Å2
Refinement stepCycle: final / Resolution: 1.8→42.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 47 369 2751
Biso mean--19.38 25.46 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062528
X-RAY DIFFRACTIONf_angle_d0.8483436
X-RAY DIFFRACTIONf_chiral_restr0.056393
X-RAY DIFFRACTIONf_plane_restr0.005447
X-RAY DIFFRACTIONf_dihedral_angle_d18.9631560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.25581210.1871244136583
1.8419-1.8880.264990.16851308140784
1.888-1.9390.19441320.151319145188
1.939-1.99610.18161320.14491357148989
1.9961-2.06050.20531420.13631402154494
2.0605-2.13410.18681620.13471396155894
2.1341-2.21960.20071210.14061505162697
2.2196-2.32060.19621220.13941477159997
2.3206-2.44290.19111360.14371475161197
2.4429-2.5960.20171260.1381499162598
2.596-2.79640.16261260.13741512163898
2.7964-3.07770.18051470.13911483163099
3.0777-3.52290.16521600.12931472163299
3.5229-4.43770.13561640.11641500166499
4.4377-42.30820.1671430.14261506164999
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)
10.605-0.1014-0.0481.21350.11250.92150.02040.03510.0305-0.0653-0.0424-0.0399-0.03870.01490.01720.03510.00540.00280.0520.01250.0388-4.31925.5336-5.6091
21.9185-0.33331.50740.89080.20422.76380.17130.0503-0.06490.01080.0008-0.0620.19380.1584-0.15820.0297-0.02090.02390.03860.00550.0445.8119-10.47220.7635
31.0872-1.7453-1.8972.87293.21234.2518-0.1111-0.1433-0.01470.22430.1010.0330.26310.04070.02160.0618-0.01160.00170.0828-0.00670.0581-1.6274-6.439618.1215
41.0664-0.0132-0.29731.17880.11991.5892-0.0022-0.0144-0.02330.1268-0.05320.08070.0057-0.07050.04950.0322-0.0028-0.01090.06280.01090.0367-7.87472.76213.1165
51.84610.1203-0.04582.06360.60141.69210.04460.00830.03260.0242-0.0252-0.1128-0.00220.03-0.01130.01740.0018-0.01240.03780.01810.04259.156-7.36783.1437
67.1049-0.991-1.17340.194-0.0071.28480.0946-0.19960.13390.02710.0624-0.00380.1046-0.0908-0.12530.0813-0.0143-0.00080.0697-0.00790.0835-7.3575-18.4445-7.847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 117 )A0 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 147 )A118 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 170 )A148 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 249 )A171 - 249
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 284 )A250 - 284
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 299 )A285 - 299

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