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- PDB-5ebv: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 5ebv
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor 11c and CoA
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / Aminoglycoside / Resistance / Tuberculosis / 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-5LR / COENZYME A / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsGajadeera, C.S. / Hou, C. / 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: 2016
Title: Potent Inhibitors of Acetyltransferase Eis Overcome Kanamycin Resistance in Mycobacterium tuberculosis.
Authors: Willby, M.J. / Green, K.D. / Gajadeera, C.S. / Hou, C. / Tsodikov, O.V. / Posey, J.E. / Garneau-Tsodikova, S.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2324
Polymers45,9991
Non-polymers1,2333
Water3,441191
1
A: Enhanced intracellular survival protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)283,39224
Polymers275,9956
Non-polymers7,39818
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 area26530 Å2
ΔGint-109 kcal/mol
Surface area86990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.168, 175.168, 122.320
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 Enhanced intracellular survival protein


Mass: 45999.113 Da / Num. of mol.: 1 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFK7
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-5LR / 5-(4-chlorophenyl)-~{N}-[3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)propyl]-4-methyl-1,1-bis(oxidanylidene)-1,2-thiazol-3-amine


Mass: 429.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN3O2S
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Reservoir: Tris-HCl pH 8.5 adjusted at room temperature (100 mM), PEG 8,000 (10-15% w/v), and (NH4)2SO4 (0.4 M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36628 / % possible obs: 99.9 % / Redundancy: 9.5 % / Net I/σ(I): 21.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.972 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1840 5 %RANDOM
Rwork0.19304 ---
obs0.19418 34661 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.813 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0.86 Å20 Å2
2---1.71 Å20 Å2
3---5.56 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 49 191 3287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193165
X-RAY DIFFRACTIONr_bond_other_d0.0010.023003
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9794310
X-RAY DIFFRACTIONr_angle_other_deg0.75636854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4221.348141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55615481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3071540
X-RAY DIFFRACTIONr_chiral_restr0.150.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
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_it1.613.3231582
X-RAY DIFFRACTIONr_mcbond_other1.6093.3231581
X-RAY DIFFRACTIONr_mcangle_it2.8124.9711974
X-RAY DIFFRACTIONr_mcangle_other2.8124.9721975
X-RAY DIFFRACTIONr_scbond_it1.8633.6411583
X-RAY DIFFRACTIONr_scbond_other1.8623.6441584
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1525.3552337
X-RAY DIFFRACTIONr_long_range_B_refined5.78527.1023493
X-RAY DIFFRACTIONr_long_range_B_other5.79926.9363453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 131 -
Rwork0.27 2528 -
obs--99.33 %

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