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- PDB-6x6y: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 6x6y
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT1264
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 suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity / biological process involved in interaction with host / host cell cytoplasmic vesicle / peptide-lysine-N-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 / N-[4-(4-fluorophenyl)-4-oxobutyl]guanidine / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 29, 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)47,07312
Polymers45,9991
Non-polymers1,07411
Water4,143230
1
AAA: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)282,43772
Polymers275,9956
Non-polymers6,44266
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 area37940 Å2
ΔGint-64 kcal/mol
Surface area86160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.483, 175.483, 124.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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 , 6 types, 241 molecules

#2: Chemical ChemComp-USY / N-[4-(4-fluorophenyl)-4-oxobutyl]guanidine


Mass: 223.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14FN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 13% PEG 8000 and 0.4 M (NH4)2SO4, 5mM kanamycin, 4 mM CoA. On soaking, replace CoA, KAN and (NH4)2SO4 with 0.5 mM inhibitor

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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: 2.5→50 Å / Num. obs: 25879 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 1279 / CC1/2: 0.78

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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: 2.5→39.966 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.463 / SU ML: 0.171 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2131 1297 5.096 %
Rwork0.1736 24156 -
all0.176 --
obs-25453 99.406 %
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: 35.856 Å2
Baniso -1Baniso -2Baniso -3
1--1.854 Å2-0.927 Å2-0 Å2
2---1.854 Å2-0 Å2
3---6.015 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 68 230 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172982
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.6514281
X-RAY DIFFRACTIONr_angle_other_deg1.1491.5756826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.07518.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40115482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3461541
X-RAY DIFFRACTIONr_chiral_restr0.0550.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
X-RAY DIFFRACTIONr_nbd_refined0.1880.2478
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22661
X-RAY DIFFRACTIONr_nbtor_refined0.150.21458
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21484
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.213
X-RAY DIFFRACTIONr_nbd_other0.1830.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0590.211
X-RAY DIFFRACTIONr_mcbond_it1.873.6011567
X-RAY DIFFRACTIONr_mcbond_other1.873.6011566
X-RAY DIFFRACTIONr_mcangle_it3.1995.3921955
X-RAY DIFFRACTIONr_mcangle_other3.1985.3911956
X-RAY DIFFRACTIONr_scbond_it2.41341594
X-RAY DIFFRACTIONr_scbond_other2.41241595
X-RAY DIFFRACTIONr_scangle_it4.0235.8172326
X-RAY DIFFRACTIONr_scangle_other4.0225.8182327
X-RAY DIFFRACTIONr_lrange_it6.13940.5033233
X-RAY DIFFRACTIONr_lrange_other6.11540.393209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.565-2.6350.343820.2941724X-RAY DIFFRACTION99.559
2.635-2.7110.29790.2761693X-RAY DIFFRACTION99.8873
2.711-2.7940.268950.2681635X-RAY DIFFRACTION99.8269
2.794-2.8850.298940.2311569X-RAY DIFFRACTION99.8199
2.885-2.9860.27960.1991521X-RAY DIFFRACTION100
2.986-3.0980.193800.1771465X-RAY DIFFRACTION99.9353
3.098-3.2230.207810.1711427X-RAY DIFFRACTION99.2758
3.223-3.3660.23710.1641367X-RAY DIFFRACTION99.5156
3.366-3.5290.219750.1491304X-RAY DIFFRACTION99.3516
3.529-3.7180.197670.151241X-RAY DIFFRACTION99.0909
3.718-3.9410.173570.141182X-RAY DIFFRACTION99.3585
3.941-4.2110.2570.1441123X-RAY DIFFRACTION99.4103
4.211-4.5440.138440.1271043X-RAY DIFFRACTION99.1788
4.544-4.9710.195590.126936X-RAY DIFFRACTION98.1262
4.971-5.5470.188440.153850X-RAY DIFFRACTION96.7532
5.547-6.3850.21370.159771X-RAY DIFFRACTION99.2629
6.385-7.770.176320.147683X-RAY DIFFRACTION100
7.77-10.7870.138290.12523X-RAY DIFFRACTION99.1023

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