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- PDB-5iv0: Crystal structure of Eis from Mycobacterium tuberculosis in compl... -

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Basic information

Entry
Database: PDB / ID: 5iv0
TitleCrystal structure of Eis from Mycobacterium tuberculosis in complex with sulfonamide inhibitor 39 and coenzyme A
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / Acetyltransferase / Inhibitor / 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 / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / N-acetyltransferase activity / 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 / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / 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 / 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
Chem-6E9 / COENZYME A / N-acetyltransferase Eis / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: J. Med. Chem. / Year: 2016
Title: Sulfonamide-Based Inhibitors of Aminoglycoside Acetyltransferase Eis Abolish Resistance to Kanamycin in Mycobacterium tuberculosis.
Authors: Garzan, A. / Willby, M.J. / Green, K.D. / Gajadeera, C.S. / Hou, C. / Tsodikov, O.V. / Posey, J.E. / Garneau-Tsodikova, S.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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

Downloads & links

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Assembly

Deposited unit
A: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8966
Polymers46,6611
Non-polymers1,2355
Water4,270237
1
A: Enhanced intracellular survival protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)287,37736
Polymers279,9656
Non-polymers7,41230
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 area29630 Å2
ΔGint-142 kcal/mol
Surface area86240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.800, 174.800, 121.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-797-

HOH

21A-837-

HOH

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Components

#1: Protein Enhanced intracellular survival protein


Mass: 46660.840 Da / Num. of mol.: 1 / Mutation: Cys204Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: eis, MT2489 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WFK6, UniProt: P9WFK7*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-6E9 / N-(3-methoxyphenyl)-N-methyl-2,3-dioxo-1,2,3,4-tetrahydroquinoxaline-6-sulfonamide


Mass: 361.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O5S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence of the construct derives from Pubmed/NCBI entry NP_216932.2, where Cys204 was mutated ...The sequence of the construct derives from Pubmed/NCBI entry NP_216932.2, where Cys204 was mutated to an Ala. This is Eis from M. tuberculosis H37Rv, hence differences from P9WFK6, an Eis homolog from a different M. tuberculosis strain.

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 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: 2.1→50 Å / Num. obs: 37907 / % possible obs: 95.8 % / Redundancy: 3.9 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.902 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21924 2002 5 %RANDOM
Rwork0.19198 ---
obs0.19333 37907 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.039 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å2-0.8 Å20 Å2
2---1.6 Å20 Å2
3---5.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 50 237 3334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193162
X-RAY DIFFRACTIONr_bond_other_d0.0010.022995
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9784305
X-RAY DIFFRACTIONr_angle_other_deg0.75436832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00321.348141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59415481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2341540
X-RAY DIFFRACTIONr_chiral_restr0.1510.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02755
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_it1.4953.3851583
X-RAY DIFFRACTIONr_mcbond_other1.4963.3851581
X-RAY DIFFRACTIONr_mcangle_it2.5975.0641974
X-RAY DIFFRACTIONr_mcangle_other2.5965.0641975
X-RAY DIFFRACTIONr_scbond_it1.833.6441579
X-RAY DIFFRACTIONr_scbond_other1.833.6441575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0585.3632323
X-RAY DIFFRACTIONr_long_range_B_refined6.05327.7363634
X-RAY DIFFRACTIONr_long_range_B_other5.90427.5123578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 152 -
Rwork0.276 2795 -
obs--97.16 %

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