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- PDB-6p3v: Crystal structure of Eis from Mycobacterium tuberculosis in compl... -

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Basic information

Entry
Database: PDB / ID: 6p3v
TitleCrystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT416
ComponentsN-acetyltransferase Eis
Keywordstransferase/transferase inhibitor / Acetyltransferase / Aminoglycoside resistance / Competitive 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 / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily ...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 / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NRV / 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)R01AI090048 United States
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis.
Authors: Green, K.D. / Punetha, A. / Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5074
Polymers45,9991
Non-polymers5083
Water1,44180
1
A: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)279,04024
Polymers275,9956
Non-polymers3,04618
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 area25680 Å2
ΔGint-135 kcal/mol
Surface area87650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.875, 174.875, 121.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#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) / Strain (production host): BL21(DE3)
References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-NRV / N,N-diethyl-2-[(8-fluoro-5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]ethan-1-amine


Mass: 333.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 3.88 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 8.0 adjusted at room temperature, 10% w/v PEG 8000, and 400 mM (NH4)2SO4

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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: Apr 12, 2019
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: 24278 / % possible obs: 97.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.654 / Num. unique obs: 1210 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.5→34.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21977 1277 5.3 %RANDOM
Rwork0.18376 ---
obs0.18575 22900 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-1.17 Å2-0 Å2
2---2.34 Å2-0 Å2
3---7.58 Å2
Refinement stepCycle: 1 / Resolution: 2.5→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 32 80 3150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133137
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172930
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6564265
X-RAY DIFFRACTIONr_angle_other_deg2.3331.5746711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.30618.84181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28315481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3271540
X-RAY DIFFRACTIONr_chiral_restr0.0670.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023570
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02742
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_it2.3544.0751573
X-RAY DIFFRACTIONr_mcbond_other2.3544.0751572
X-RAY DIFFRACTIONr_mcangle_it3.8696.0981961
X-RAY DIFFRACTIONr_mcangle_other3.8686.0981962
X-RAY DIFFRACTIONr_scbond_it2.8644.4451564
X-RAY DIFFRACTIONr_scbond_other2.8634.4491565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7086.4992305
X-RAY DIFFRACTIONr_long_range_B_refined6.73145.2133289
X-RAY DIFFRACTIONr_long_range_B_other6.69245.5193199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 104 -
Rwork0.296 1640 -
obs--97.87 %

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