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- PDB-6b0u: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 6b0u
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with a Lys-containing peptide
Components
  • N-acetyltransferase Eis
  • Synthetic peptide ATKAPAKKA
KeywordsTRANSFERASE / histone acetylation / aminoglycoside / drug resistance / tuberculosis / acetylation
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
COENZYME A / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBiswas, T. / Pang, A.H. / 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: Biochemistry / Year: 2018
Title: Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight.
Authors: Green, K.D. / Biswas, T. / Pang, A.H. / Willby, M.J. / Reed, M.S. / Stuchlik, O. / Pohl, J. / Posey, J.E. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionSep 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: N-acetyltransferase Eis
B: N-acetyltransferase Eis
C: N-acetyltransferase Eis
D: Synthetic peptide ATKAPAKKA
E: Synthetic peptide ATKAPAKKA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,69310
Polymers141,8555
Non-polymers3,8385
Water0
1
A: N-acetyltransferase Eis
B: N-acetyltransferase Eis
C: N-acetyltransferase Eis
D: Synthetic peptide ATKAPAKKA
E: Synthetic peptide ATKAPAKKA
hetero molecules

A: N-acetyltransferase Eis
B: N-acetyltransferase Eis
C: N-acetyltransferase Eis
D: Synthetic peptide ATKAPAKKA
E: Synthetic peptide ATKAPAKKA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,38520
Polymers283,71010
Non-polymers7,67510
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Unit cell
Length a, b, c (Å)109.902, 175.866, 85.129
Angle α, β, γ (deg.)90.00, 120.49, 90.00
Int Tables number5
Space group name H-MC121

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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: 46692.902 Da / Num. of mol.: 3
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
#2: Protein/peptide Synthetic peptide ATKAPAKKA


Mass: 888.084 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: peptide (1 mM) and CoA (1 mM) with protein in a 1:1 ration with reservoir solution (Tris-HCl (100 mM, pH 8.5) and PEG 8,000 (13% w/v))

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→37.71 Å / Num. obs: 30053 / % possible obs: 87 % / Observed criterion σ(I): 2.8 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.24 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.8→37 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.379 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25953 1486 5 %RANDOM
Rwork0.21192 ---
obs0.21424 28341 87.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.785 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.11 Å2
2--0.21 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.8→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 87 0 9223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199432
X-RAY DIFFRACTIONr_bond_other_d0.0010.028847
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.97212818
X-RAY DIFFRACTIONr_angle_other_deg0.887320272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66751173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12421.321424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.067151463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.60515121
X-RAY DIFFRACTIONr_chiral_restr0.0650.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022117
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_it1.9946.0054725
X-RAY DIFFRACTIONr_mcbond_other1.9946.0044724
X-RAY DIFFRACTIONr_mcangle_it3.478.9925887
X-RAY DIFFRACTIONr_mcangle_other3.478.9935888
X-RAY DIFFRACTIONr_scbond_it1.8126.2454707
X-RAY DIFFRACTIONr_scbond_other1.8036.2454707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.149.2856932
X-RAY DIFFRACTIONr_long_range_B_refined5.53568.7269678
X-RAY DIFFRACTIONr_long_range_B_other5.53468.7329679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 109 -
Rwork0.377 2148 -
obs--89.99 %

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