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- PDB-6moo: Co-Crystal structure of P. aeruginosa LpxC-achn975 complex -

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Basic information

Entry
Database: PDB / ID: 6moo
TitleCo-Crystal structure of P. aeruginosa LpxC-achn975 complex
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE/INHIBITOR / Hydrolase LpxC Pseudomonas aeruginosa / 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-A5F / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStein, A.J. / Assar, Z. / Holt, M.C. / Cohen, F. / Andrews, L. / Cirz, R.
CitationJournal: Chemmedchem / Year: 2019
Title: Optimization of LpxC Inhibitors for Antibacterial Activity and Cardiovascular Safety.
Authors: Cohen, F. / Aggen, J.B. / Andrews, L.D. / Assar, Z. / Boggs, J. / Choi, T. / Dozzo, P. / Easterday, A.N. / Haglund, C.M. / Hildebrandt, D.J. / Holt, M.C. / Joly, K. / Jubb, A. / Kamal, Z. / ...Authors: Cohen, F. / Aggen, J.B. / Andrews, L.D. / Assar, Z. / Boggs, J. / Choi, T. / Dozzo, P. / Easterday, A.N. / Haglund, C.M. / Hildebrandt, D.J. / Holt, M.C. / Joly, K. / Jubb, A. / Kamal, Z. / Kane, T.R. / Konradi, A.W. / Krause, K.M. / Linsell, M.S. / Machajewski, T.D. / Miroshnikova, O. / Moser, H.E. / Nieto, V. / Phan, T. / Plato, C. / Serio, A.W. / Seroogy, J. / Shakhmin, A. / Stein, A.J. / Sun, A.D. / Sviridov, S. / Wang, Z. / Wlasichuk, K. / Yang, W. / Zhou, X. / Zhu, H. / Cirz, R.T.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1423
Polymers33,7071
Non-polymers4352
Water1,13563
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)35.887, 66.860, 63.728
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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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: 33707.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lpxC_1, lpxC, C0044_32665, C8257_27020, CAZ10_21290, CGU42_01150, CW299_32585, DI492_11215, DN070_30465, DT376_11200, NCTC13719_04761, PAERUG_E15_London_28_01_14_00522, RW109_RW109_05745
Production host: Escherichia coli (E. coli)
References: UniProt: A0A072ZC86, UniProt: P47205*PLUS, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A5F / N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide / ACHN-975


Mass: 369.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350 and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→19.49 Å / Num. obs: 14425 / % possible obs: 99.09 % / Redundancy: 2 % / CC1/2: 0.918 / Net I/σ(I): 9.12
Reflection shellResolution: 2.2→2.26 Å / CC1/2: 0.983

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3D

4j3d


Resolution: 2.2→19.49 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.83 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23888 759 5 %RANDOM
Rwork0.17628 ---
obs0.17938 14425 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.04 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.2→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 28 63 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192383
X-RAY DIFFRACTIONr_bond_other_d0.0010.022290
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9743225
X-RAY DIFFRACTIONr_angle_other_deg0.90435252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89824.057106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6451516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0642.4391202
X-RAY DIFFRACTIONr_mcbond_other2.0522.4361201
X-RAY DIFFRACTIONr_mcangle_it3.0653.6461500
X-RAY DIFFRACTIONr_mcangle_other3.0643.6471501
X-RAY DIFFRACTIONr_scbond_it2.932.8551181
X-RAY DIFFRACTIONr_scbond_other2.9292.8551181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5814.1271723
X-RAY DIFFRACTIONr_long_range_B_refined5.82219.5182537
X-RAY DIFFRACTIONr_long_range_B_other5.80119.492523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.204→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 58 -
Rwork0.225 951 -
obs--90.49 %

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