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- PDB-6x6g: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 6x6g
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with droperidol
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 / Chem-USS / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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)47,10110
Polymers45,9991
Non-polymers1,1029
Water6,035335
1
AAA: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)282,60860
Polymers275,9956
Non-polymers6,61454
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 area34910 Å2
ΔGint-1 kcal/mol
Surface area85680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.010, 175.010, 124.465
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-928-

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, 344 molecules

#2: Chemical ChemComp-USS / 3-[1-[4-(4-fluorophenyl)-4-oxidanylidene-butyl]-2,3,4,5-tetrahydropyridin-4-yl]-1~{H}-benzimidazol-2-one / droperidol


Mass: 379.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22FN3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antipsychotic*YM
#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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.99 Å3/Da / Density % sol: 69.15 %
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). Replace 0.4 M (NH4)2SO4; KAN (5 mM) with 0.5 mM inhibitor in soaking crystals.

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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: 2.15→50 Å / Num. obs: 39772 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 19
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.65 / Num. unique obs: 1994 / 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: 2.15→40.003 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.455 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2055 1929 4.89 %
Rwork0.1732 37520 -
all0.175 --
obs-39449 99.225 %
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: 35.444 Å2
Baniso -1Baniso -2Baniso -3
1--1.575 Å2-0.788 Å20 Å2
2---1.575 Å20 Å2
3---5.11 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 73 335 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133163
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172965
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.6594287
X-RAY DIFFRACTIONr_angle_other_deg1.2341.5746788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.98418.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39115481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6671541
X-RAY DIFFRACTIONr_chiral_restr0.0580.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined0.1890.2537
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22697
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21468
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.216
X-RAY DIFFRACTIONr_nbd_other0.2050.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.225
X-RAY DIFFRACTIONr_mcbond_it1.8133.4891562
X-RAY DIFFRACTIONr_mcbond_other1.8113.4891561
X-RAY DIFFRACTIONr_mcangle_it2.9635.2211948
X-RAY DIFFRACTIONr_mcangle_other2.9625.2211949
X-RAY DIFFRACTIONr_scbond_it2.3623.9491601
X-RAY DIFFRACTIONr_scbond_other2.3613.9481602
X-RAY DIFFRACTIONr_scangle_it3.8825.7612339
X-RAY DIFFRACTIONr_scangle_other3.8815.762340
X-RAY DIFFRACTIONr_lrange_it6.58242.0323465
X-RAY DIFFRACTIONr_lrange_other6.35141.4193392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.15-2.2060.2751560.27427390.27428950.7780.7691000.253
2.206-2.2660.2641250.25527320.25528570.7910.81000.23
2.266-2.3310.2481330.22826370.22927730.8530.87299.89180.199
2.331-2.4030.2151400.21124970.21126410.9010.90899.84850.182
2.403-2.4810.2541340.19324840.19626210.9070.92599.88550.171
2.481-2.5680.2491200.19223760.19424990.9090.92399.880.166
2.568-2.6650.2641150.19423250.19724530.9080.92699.470.168
2.665-2.7730.221190.18421540.18623300.9220.93497.55360.158
2.773-2.8960.2211010.18721240.18922520.940.94198.80110.164
2.896-3.0360.213930.16920770.17121720.9450.95599.90790.149
3.036-3.1990.196870.16319410.16520300.9390.95699.90150.149
3.199-3.3920.196880.16518370.16619320.9530.95899.63770.154
3.392-3.6240.2161140.16117090.16418390.9470.95999.130.156
3.624-3.9120.171680.1516350.15117080.9610.96899.70730.145
3.912-4.2810.166710.14714730.14815680.9710.97298.46940.148
4.281-4.780.145780.13313260.13314330.9750.97897.97630.142
4.78-5.5060.163780.14511320.14612760.9750.97394.82760.154
5.506-6.7120.234500.17510190.17810780.9310.9699.16510.187
6.712-9.3620.207340.1628160.1648650.9510.96398.26590.186
9.362-40.0030.238250.1784800.1815180.9330.96197.49030.209

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