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

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Basic information

Entry
Database: PDB / ID: 5tvj
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with CoA and inhibitor 2k*: 1-(4-fluorophenyl)-2-[2-(4-methylphenyl)-2-oxoethyl]pyrrolo[1,2-a]pyrazin-2-ium
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / TRANSFERASE / acetyltransferase / resistance / aminoglycoside / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host programmed cell death / 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 / bacterial extracellular vesicle / biological process involved in interaction with host ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host programmed cell death / 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 / bacterial extracellular vesicle / biological process involved in interaction with host / host cell cytoplasmic vesicle / N-acetyltransferase activity / 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 / Gcn5-related N-acetyltransferase (GNAT) ...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-7LF / COENZYME A / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGajadeera, C.S. / Garzan, A. / 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 Infect Dis / Year: 2017
Title: Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors.
Authors: Garzan, A. / Willby, M.J. / Ngo, H.X. / Gajadeera, C.S. / Green, K.D. / Holbrook, S.Y. / Hou, C. / Posey, J.E. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2405
Polymers45,9991
Non-polymers1,2404
Water1,60389
1
A: Enhanced intracellular survival protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)283,43830
Polymers275,9956
Non-polymers7,44324
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 area31280 Å2
ΔGint-106 kcal/mol
Surface area88330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.106, 175.106, 122.940
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 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WFK7

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-7LF / 1-(4-fluorophenyl)-2-[2-(4-methylphenyl)-2-oxoethyl]pyrrolo[1,2-a]pyrazin-2-ium


Mass: 345.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18FN2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: RESERVOIR: TRIS-HCL PH 8.5 ADJUSTED AT REMARK 280 ROOM TEMPERATURE (100 MM), PEG 8,000 (10-15% W/V), AND (NH4)2SO4 REMARK 280 (0.4 M), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 30515 / % possible obs: 99.8 % / Redundancy: 7.3 % / Net I/σ(I): 24

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.191 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22365 1615 5 %RANDOM
Rwork0.19183 ---
obs0.19342 30515 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.855 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å2-1.13 Å20 Å2
2---2.25 Å20 Å2
3---7.31 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 81 89 3217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193199
X-RAY DIFFRACTIONr_bond_other_d0.0010.023022
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.994357
X-RAY DIFFRACTIONr_angle_other_deg0.88336900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08421.348141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50515481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8231540
X-RAY DIFFRACTIONr_chiral_restr0.1780.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213606
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02770
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_it2.2824.7521583
X-RAY DIFFRACTIONr_mcbond_other2.2824.7521581
X-RAY DIFFRACTIONr_mcangle_it3.7927.1161975
X-RAY DIFFRACTIONr_mcangle_other3.7927.1161976
X-RAY DIFFRACTIONr_scbond_it2.755.281616
X-RAY DIFFRACTIONr_scbond_other2.7445.281616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5397.7762383
X-RAY DIFFRACTIONr_long_range_B_refined7.20839.0863446
X-RAY DIFFRACTIONr_long_range_B_other7.239.0573438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 117 -
Rwork0.277 2208 -
obs--98.31 %

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