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- PDB-6vv1: Crystal structure of Eis from Mycobacterium tuberculosis in compl... -

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Basic information

Entry
Database: PDB / ID: 6vv1
TitleCrystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT384
ComponentsN-acetyltransferase Eis
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Acetyltransferase / Resistance / Aminoglycoside / Competitive / 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 / Suppression of autophagy / symbiont-mediated suppression of host programmed cell death / 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 / Suppression of autophagy / symbiont-mediated suppression of host programmed cell death / 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 / SCP2 sterol-binding domain / Acetyltransferase (GNAT) 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 / SCP2 sterol-binding domain / Acetyltransferase (GNAT) 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
DI(HYDROXYETHYL)ETHER / Chem-RMJ / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPunetha, A. / Hou, C. / Ngo, H.X. / 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: Acs Chem.Biol. / Year: 2020
Title: Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis.
Authors: Punetha, A. / Ngo, H.X. / Holbrook, S.Y.L. / Green, K.D. / Willby, M.J. / Bonnett, S.A. / Krieger, K. / Dennis, E.K. / Posey, J.E. / Parish, T. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionFeb 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: 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 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

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Assembly

Deposited unit
A: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,34713
Polymers45,9991
Non-polymers1,34812
Water4,486249
1
A: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)284,08078
Polymers275,9956
Non-polymers8,08572
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 area37210 Å2
ΔGint-282 kcal/mol
Surface area87780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.329, 175.329, 124.229
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 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 (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 , 7 types, 261 molecules

#2: Chemical ChemComp-RMJ / 2-[(4-amino-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(piperidin-1-yl)ethyl]acetamide


Mass: 391.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25N5OS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 69.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 8.0 adjusted at room temperature, 7% 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 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 26373 / % possible obs: 97.5 % / Redundancy: 6.1 % / CC1/2: 1 / Rmerge(I) obs: 0.113 / Net I/σ(I): 19.1
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.908 / Num. unique obs: 1343 / CC1/2: 0.786 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.45→36.33 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.168 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.202
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1340 5.1 %RANDOM
Rwork0.1692 ---
obs0.1716 24898 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.74 Å2 / Biso mean: 42.912 Å2 / Biso min: 22.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0.82 Å2-0 Å2
2---1.64 Å2-0 Å2
3---5.32 Å2
Refinement stepCycle: final / Resolution: 2.45→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 82 249 3378
Biso mean--82.44 47.98 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133189
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172976
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6564325
X-RAY DIFFRACTIONr_angle_other_deg1.171.5746816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.41718.84181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61415481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7841540
X-RAY DIFFRACTIONr_chiral_restr0.0590.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02745
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 87 -
Rwork0.257 1870 -
all-1957 -
obs--99.14 %

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