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- PDB-6x6i: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 6x6i
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT543
ComponentsN-acetyltransferase Eis
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Aminoglycoside / Drug resistance / Repurposing / Acetylation / Inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated perturbation of host innate immune response / symbiont-mediated suppression of host programmed cell death / Suppression of autophagy / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / biological process involved in interaction with host ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated perturbation of host innate immune response / symbiont-mediated suppression of host programmed cell death / Suppression of autophagy / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / biological process involved in interaction with host / N-acetyltransferase activity / host cell cytoplasmic vesicle / protein-lysine-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / host extracellular space / response to antibiotic / identical protein binding / cytosol
Similarity search - Function
N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-USG / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsPunetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090048 United States
CitationJournal: Rsc Med Chem / Year: 2021
Title: Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance
Authors: Punetha, A. / Green, K.D. / Garzan, A. / Willby, M.J. / Pang, A.H. / Hou, C. / Holbrook, S.Y.L. / Krieger, K. / Posey, J.E. / Parish, T. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9759
Polymers45,9991
Non-polymers9758
Water7,062392
1
AAA: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)281,84854
Polymers275,9956
Non-polymers5,85348
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area33920 Å2
ΔGint-103 kcal/mol
Surface area84820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.027, 175.027, 124.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-969-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein N-acetyltransferase Eis / Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N- ...Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N-acetyltransferase


Mass: 45999.113 Da / Num. of mol.: 1 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 400 molecules

#2: Chemical ChemComp-USG / 4-(4-benzyl-4-hydroxypiperidin-1-yl)-1-(4-fluorophenyl)butan-1-one


Mass: 373.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25F2NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 13% PEG 8000 and 0.4 M (NH4)2SO4; KAN (5 mM) and CoA (4 mM) in drop. Replace 0.4 M (NH4)2SO4; KAN (5 mM) and CoA (4 mM) with 0.5 mM inhibitor upon soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 56009 / % possible obs: 98.7 % / Redundancy: 7.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.3
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.96 / Num. unique obs: 2793 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X10

6x10


Resolution: 1.904→37.435 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.977 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1997 2762 4.942 %
Rwork0.1741 53121 -
all0.175 --
obs-55883 98.133 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.297 Å2
Baniso -1Baniso -2Baniso -3
1--1.259 Å2-0.63 Å2-0 Å2
2---1.259 Å2-0 Å2
3---4.085 Å2
Refinement stepCycle: LAST / Resolution: 1.904→37.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 58 392 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133149
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172959
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.6554270
X-RAY DIFFRACTIONr_angle_other_deg1.2461.5746779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.14718.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6911541
X-RAY DIFFRACTIONr_chiral_restr0.0580.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined0.1860.2518
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22629
X-RAY DIFFRACTIONr_nbtor_refined0.1540.21479
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21385
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2309
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.130.217
X-RAY DIFFRACTIONr_nbd_other0.170.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.233
X-RAY DIFFRACTIONr_mcbond_it1.572.8381561
X-RAY DIFFRACTIONr_mcbond_other1.5692.8381560
X-RAY DIFFRACTIONr_mcangle_it2.5714.2411946
X-RAY DIFFRACTIONr_mcangle_other2.5714.2411947
X-RAY DIFFRACTIONr_scbond_it2.0043.191588
X-RAY DIFFRACTIONr_scbond_other2.0043.1921589
X-RAY DIFFRACTIONr_scangle_it3.3244.6472324
X-RAY DIFFRACTIONr_scangle_other3.3244.6482325
X-RAY DIFFRACTIONr_lrange_it5.94534.8273492
X-RAY DIFFRACTIONr_lrange_other5.63933.6563374
LS refinement shellResolution: 1.904→1.953 Å
RfactorNum. reflection% reflection
Rfree0.26 198 -
Rwork0.26 3791 -
obs--95.1801 %

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