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- PDB-5u3b: Pseudomonas aeruginosa LpxC in complex with NVS-LPXC-01 -

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Basic information

Entry
Database: PDB / ID: 5u3b
TitlePseudomonas aeruginosa LpxC in complex with NVS-LPXC-01
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LPXC / HYDROXYMATE / GRAM NEGATIVE
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
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-7TD / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSprague, E.R.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design, Synthesis, and Properties of a Potent Inhibitor of Pseudomonas aeruginosa Deacetylase LpxC.
Authors: Piizzi, G. / Parker, D.T. / Peng, Y. / Dobler, M. / Patnaik, A. / Wattanasin, S. / Liu, E. / Lenoir, F. / Nunez, J. / Kerrigan, J. / McKenney, D. / Osborne, C. / Yu, D. / Lanieri, L. / ...Authors: Piizzi, G. / Parker, D.T. / Peng, Y. / Dobler, M. / Patnaik, A. / Wattanasin, S. / Liu, E. / Lenoir, F. / Nunez, J. / Kerrigan, J. / McKenney, D. / Osborne, C. / Yu, D. / Lanieri, L. / Bojkovic, J. / Dzink-Fox, J. / Lilly, M.D. / Sprague, E.R. / Lu, Y. / Wang, H. / Ranjitkar, S. / Xie, L. / Wang, B. / Glick, M. / Hamann, L.G. / Tommasi, R. / Yang, X. / Dean, C.R.
History
DepositionDec 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5728
Polymers66,3252
Non-polymers1,2466
Water5,080282
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7864
Polymers33,1631
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7864
Polymers33,1631
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.826, 98.432, 165.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 33162.680 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 (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-7TD / N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[(but-2-yn-1-yl)oxy]benzamide


Mass: 319.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes PH 7.0, 0.25M MgCl2, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→82.59 Å / Num. obs: 40521 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.11 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.59 Å / Redundancy: 5.4 % / Rmerge F obs: 0.019 / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 2863 / Num. possible: 534 / Num. unique obs: 532 / Rrim(I) all: 0.034 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→82.59 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9341 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.191 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.149 / Details: Initial refinement with Phenix
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2026 5 %RANDOM
Rwork0.1861 ---
obs0.1874 40520 99.83 %-
Displacement parametersBiso max: 114.07 Å2 / Biso mean: 28.74 Å2 / Biso min: 11.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.1796 Å20 Å20 Å2
2--3.6653 Å20 Å2
3----3.8449 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: final / Resolution: 2→82.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4615 0 78 282 4975
Biso mean--29.85 33.14 -
Num. residues----591
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1699SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes687HARMONIC5
X-RAY DIFFRACTIONt_it4768HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion617SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5661SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4768HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6441HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion15.89
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2717 146 5 %
Rwork0.2165 2776 -
all0.2193 2922 -
obs--99.83 %
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)
10.65260.2117-0.02760.76540.09570.6068-0.01780.0479-0.0319-0.0632-0.01350.00030.05070.01410.03130.01260.00880.00370.0017-0.00880.026415.5507-7.14518.465
20.4379-0.22-0.04250.7730.19370.5387-0.0042-0.0249-0.00860.0537-0.04140.0110.0080.00120.04560.0092-0.01430.00330.01850.00050.0257.47268.0865-21.0491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 299
2X-RAY DIFFRACTION2{ B|* }B1 - 299

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