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- PDB-7ci7: Crystal structure of P.aeruginosa LpxC in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 7ci7
TitleCrystal structure of P.aeruginosa LpxC in complex with inhibitor
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / UDP-3-O-acyl-N-acetylglucosamine deacetylase / EnvA / LpxC / Pseudomonas aeruginosa
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
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-type fold
Similarity search - Domain/homology
Chem-FY9 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMima, M. / Baker, L.M. / Surgenor, A. / Robertson, A.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity.
Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / ...Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / Ohtake, N. / Angove, H. / Baker, L. / Harris, R. / Macias, A. / Robertson, A. / Surgenor, A. / Watanabe, H. / Nakano, K. / Mima, M. / Iwamoto, K. / Okada, A. / Takata, I. / Hitaka, K. / Tanaka, A. / Fujita, K. / Sugiyama, H. / Hubbard, R.E.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6973
Polymers33,1471
Non-polymers5502
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13340 Å2
Unit cell
Length a, b, c (Å)35.716, 67.046, 63.258
Angle α, β, γ (deg.)90.00, 90.96, 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: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli (E. coli)
References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-FY9 / (2R,3R)-2-azanyl-1-[4-[[4-[2-[4-(hydroxymethyl)phenyl]ethynyl]phenyl]methyl]piperidin-1-yl]-4-methylsulfonyl-3-oxidanyl-butan-1-one


Mass: 484.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.03M Diethylene glycol 0.03M Triethylene glycol 0.03M Tetraethylene glycol 0.03M Pentaethylene glycol 0.1M Tris - BICINE pH 8.5 20 % v/v PEG 500 MME 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.1→22.17 Å / Num. obs: 17500 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 5.92
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1750 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UHM

3uhm


Resolution: 2.1→22.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.399 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24964 957 5.5 %RANDOM
Rwork0.19388 ---
obs0.19689 16517 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.1→22.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 35 142 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132376
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172252
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6593212
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5975207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24122.222126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38315409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3541517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02506
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_it1.8282.3281178
X-RAY DIFFRACTIONr_mcbond_other1.8272.3271177
X-RAY DIFFRACTIONr_mcangle_it2.9293.4781469
X-RAY DIFFRACTIONr_mcangle_other2.9283.481470
X-RAY DIFFRACTIONr_scbond_it2.3162.7531198
X-RAY DIFFRACTIONr_scbond_other2.3152.7531198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7574.0071744
X-RAY DIFFRACTIONr_long_range_B_refined7.06945.52910988
X-RAY DIFFRACTIONr_long_range_B_other7.06745.50910906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 71 -
Rwork0.258 1182 -
obs--99.92 %

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