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- PDB-6c9c: Crystal structure of LpxC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6c9c
TitleCrystal structure of LpxC from Pseudomonas aeruginosa in complex with racemic ligand PT803
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / inhibitor / Structural Genomics / 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-[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-EU1 / Chem-F64 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of LpxC from Pseudomonas aeruginosa in complex with ligand PT803
Authors: Delker, S.L. / Mayclin, S.J. / Phan, J.N. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Category: pdbx_SG_project / pdbx_database_status / Item: _pdbx_database_status.SG_entry
Revision 1.2Oct 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)35,0149
Polymers33,5621
Non-polymers1,4528
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.660, 79.340, 50.920
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211

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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,PsaeA.00166.a.DG15,PsaeA.00166.a.DG15,PsaeA.00166.a.DG15
Mutation: M33V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: lpxC, PA14_57260 / Plasmid: PsaeA.00166.a.DG15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q02H34, UDP-3-O-acyl-N-acetylglucosamine deacetylase

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-EU1 / (2R)-4-[4-{4-[(5-chloro-6-methoxypyridin-3-yl)methoxy]phenyl}-2-oxo-3,6-dihydropyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 538.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN3O7S
#3: Chemical ChemComp-F64 / (2S)-4-[4-{4-[(5-chloro-6-methoxypyridin-3-yl)methoxy]phenyl}-2-oxo-3,6-dihydropyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Mass: 538.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28ClN3O7S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: tray296747a A10: 100 mM Tris-HCl, pH 8.5, 30% (w/v) Propanol, 30% (w/v) PEG 3350 +1mM ZnCl2, 1mM BSI108453 (PT803) : Cryo = 20%EG : PsaeA.00166.a.DG15.PD00471 at 5 mg/ml, puck qcu4-1

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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: Dec 7, 2017 / Details: mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→35.638 Å / Num. obs: 18652 / % possible obs: 97.1 % / Redundancy: 4.114 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.113 / Χ2: 0.964 / Net I/σ(I): 11.72 / Num. measured all: 76737 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.3870.5632.0210980.7690.66276.8
2.05-2.113.4460.4872.3712500.7960.5789.9
2.11-2.173.9570.4013.1913120.8780.46599.2
2.17-2.244.2480.3593.8812880.8980.4198.6
2.24-2.314.2890.3224.2612370.9180.36899.5
2.31-2.394.2550.265.4712370.9480.29798.6
2.39-2.484.2890.2365.9711580.9420.26999.7
2.48-2.584.2610.26.9711090.9650.22999.3
2.58-2.74.260.1688.0810970.9720.19299.5
2.7-2.834.2680.1489.3910410.9830.16999.7
2.83-2.984.2150.12211.4510020.9870.13999.5
2.98-3.164.2570.09314.499370.9910.10799.8
3.16-3.384.2590.0718.058700.9950.0899.8
3.38-3.654.2210.05422.628190.9970.06299.5
3.65-44.1980.04726.137590.9970.05399.9
4-4.474.1950.03730.966910.9980.04299.7
4.47-5.164.1940.03333.036070.9990.03899.8
5.16-6.324.1730.03830.035200.9980.044100
6.32-8.944.1270.03234.724010.9990.03799.8
8.94-35.6383.8450.02640.432190.9990.0398.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWM

5vwm


Resolution: 2→35.638 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1907 10.23 %
Rwork0.1623 --
obs0.1675 18648 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→35.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 93 171 2513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062417
X-RAY DIFFRACTIONf_angle_d1.143270
X-RAY DIFFRACTIONf_dihedral_angle_d19.811433
X-RAY DIFFRACTIONf_chiral_restr0.127365
X-RAY DIFFRACTIONf_plane_restr0.005420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30381160.2159941X-RAY DIFFRACTION76
2.05-2.10540.25971310.211094X-RAY DIFFRACTION89
2.1054-2.16740.26771220.19581202X-RAY DIFFRACTION99
2.1674-2.23730.23021420.18061221X-RAY DIFFRACTION99
2.2373-2.31730.25271400.16861207X-RAY DIFFRACTION100
2.3173-2.410.23551360.16331220X-RAY DIFFRACTION99
2.41-2.51970.22081460.16421202X-RAY DIFFRACTION100
2.5197-2.65250.23621350.17241242X-RAY DIFFRACTION100
2.6525-2.81860.23611570.16681207X-RAY DIFFRACTION99
2.8186-3.03620.21891400.16951223X-RAY DIFFRACTION100
3.0362-3.34150.25181310.15861244X-RAY DIFFRACTION100
3.3415-3.82450.17511500.15211212X-RAY DIFFRACTION100
3.8245-4.81660.15881250.12891254X-RAY DIFFRACTION100
4.8166-35.64370.18851360.16211272X-RAY DIFFRACTION100
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)
10.99850.0779-0.46220.67190.01780.9160.06260.02640.0711-0.0341-0.0069-0.0015-0.0769-0.105-0.05380.17040.0044-0.00760.19190.00930.18089.3362.85634.8267
24.6209-3.9277-0.52798.46070.26853.5524-0.1459-0.3729-0.47820.7421-0.10550.0730.58090.20730.14980.25940.00730.00340.26130.03560.18088.1586-8.673324.5389
31.2168-0.6173-0.37482.25590.90831.0741-0.0046-0.1138-0.00230.17280.0518-0.15580.04250.0367-0.04450.1425-0.0199-0.00280.17360.02390.14629.8639-7.281315.3718
45.24610.83470.84981.4373-1.85078.4621-0.3183-0.1462-0.164-0.3828-0.3296-0.29380.70650.11410.61030.36650.0311-0.00320.2138-0.04590.35518.211522.06621.8168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 299 )

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