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- PDB-8f58: Crystal structure of acetyltransferase Eis from M. tuberculosis i... -

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Basic information

Entry
Database: PDB / ID: 8f58
TitleCrystal structure of acetyltransferase Eis from M. tuberculosis in complex with inhibitor SGT1616
ComponentsN-acetyltransferase Eis
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / drug resistance / inhibitor / acetylation / 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 perturbation of host programmed cell death / Suppression of autophagy / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / N-acetyltransferase activity ...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 perturbation of host programmed cell death / Suppression of autophagy / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / N-acetyltransferase activity / biological process involved in interaction with host / 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-XEH / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPang, A.H. / Punetha, 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: Biochemistry / Year: 2023
Title: Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs.
Authors: Pang, A.H. / Green, K.D. / Punetha, A. / Thamban Chandrika, N. / Howard, K.C. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionNov 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8659
Polymers45,9991
Non-polymers8658
Water4,270237
1
A: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)281,18854
Polymers275,9956
Non-polymers5,19348
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 area33470 Å2
ΔGint41 kcal/mol
Surface area85690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.401, 175.401, 123.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#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 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, 245 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-XEH / (1E)-1-[(4-chlorophenyl)methylidene]-2-(4-fluorophenyl)hydrazine


Mass: 248.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10ClFN2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 237 / 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: 4.26 Å3/Da / Density % sol: 71.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl pH 8.5 (0.1 M), PEG 8000 (10% w/v), and (NH4)2SO4 (0.5 M)

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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: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 32274 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1594 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.3→34.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.221 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19877 1521 4.8 %RANDOM
Rwork0.17443 ---
obs0.17561 30291 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.704 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0.74 Å2-0 Å2
2---1.48 Å2-0 Å2
3---4.8 Å2
Refinement stepCycle: 1 / Resolution: 2.3→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 54 237 3313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133149
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172998
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.6454271
X-RAY DIFFRACTIONr_angle_other_deg1.31.5756845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.15118.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6611541
X-RAY DIFFRACTIONr_chiral_restr0.0610.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
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_it1.9073.6131562
X-RAY DIFFRACTIONr_mcbond_other1.9043.6131561
X-RAY DIFFRACTIONr_mcangle_it3.2325.4051949
X-RAY DIFFRACTIONr_mcangle_other3.2325.4051950
X-RAY DIFFRACTIONr_scbond_it2.5314.1031587
X-RAY DIFFRACTIONr_scbond_other2.5314.1051588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2325.9792323
X-RAY DIFFRACTIONr_long_range_B_refined6.60242.6953367
X-RAY DIFFRACTIONr_long_range_B_other6.58642.3663322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 98 -
Rwork0.278 2184 -
obs--96.04 %

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