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- PDB-9mva: Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable Coe... -

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Basic information

Entry
Database: PDB / ID: 9mva
TitleMycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA
ComponentsAmikacin resistance N-acetyltransferase Eis2
KeywordsANTIBIOTIC / Acetyl transferase
Function / homology
Function and homology information


aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity
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 superfamily / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-SOP / Amikacin resistance N-acetyltransferase Eis2
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJayasinghe, T.D. / Coker, A.L. / Rajendra, T. / Miller, D. / Lee, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA
Authors: Jayasinghe, T.D. / Coker, A.L. / Rajendra, T. / Miller, D. / Lee, R.E.
History
DepositionJan 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amikacin resistance N-acetyltransferase Eis2
B: Amikacin resistance N-acetyltransferase Eis2
C: Amikacin resistance N-acetyltransferase Eis2
D: Amikacin resistance N-acetyltransferase Eis2
E: Amikacin resistance N-acetyltransferase Eis2
F: Amikacin resistance N-acetyltransferase Eis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,76365
Polymers271,6976
Non-polymers9,06659
Water50,4782802
1
A: Amikacin resistance N-acetyltransferase Eis2
D: Amikacin resistance N-acetyltransferase Eis2
E: Amikacin resistance N-acetyltransferase Eis2
hetero molecules

A: Amikacin resistance N-acetyltransferase Eis2
D: Amikacin resistance N-acetyltransferase Eis2
E: Amikacin resistance N-acetyltransferase Eis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,53362
Polymers271,6976
Non-polymers8,83656
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
2
B: Amikacin resistance N-acetyltransferase Eis2
C: Amikacin resistance N-acetyltransferase Eis2
F: Amikacin resistance N-acetyltransferase Eis2
hetero molecules

B: Amikacin resistance N-acetyltransferase Eis2
C: Amikacin resistance N-acetyltransferase Eis2
F: Amikacin resistance N-acetyltransferase Eis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,99468
Polymers271,6976
Non-polymers9,29662
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)195.695, 209.587, 152.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21B-695-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Amikacin resistance N-acetyltransferase Eis2 / GNAT family N-acetyltransferase


Mass: 45282.855 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: eis_2, D2E76_13785, DDJ47_01400, ERS075604_03569 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A418L6F2

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Non-polymers , 7 types, 2861 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SOP / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE / S-(2-OXOPROPYL)-COENZYME A


Mass: 823.597 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2802 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgCl2, 15% PEG400, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Sep 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→34.36 Å / Num. obs: 286623 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 16.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.09 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 126307 / CC1/2: 0.997 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
SCALEPACKdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.36 Å / SU ML: 0.2209 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2215 1382 0.48 %
Rwork0.1909 284513 -
obs0.1911 285895 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18742 0 569 2802 22113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007519882
X-RAY DIFFRACTIONf_angle_d0.897727070
X-RAY DIFFRACTIONf_chiral_restr0.0543007
X-RAY DIFFRACTIONf_plane_restr0.00873495
X-RAY DIFFRACTIONf_dihedral_angle_d15.31937136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.3351300.281828339X-RAY DIFFRACTION99.94
1.86-1.940.32251440.256628304X-RAY DIFFRACTION99.91
1.94-2.030.28811320.239428329X-RAY DIFFRACTION99.92
2.03-2.130.27141420.22128333X-RAY DIFFRACTION99.85
2.13-2.270.26871330.199828343X-RAY DIFFRACTION99.86
2.27-2.440.22631370.195828394X-RAY DIFFRACTION99.85
2.44-2.690.22491350.190128450X-RAY DIFFRACTION99.79
2.69-3.080.21811380.183628481X-RAY DIFFRACTION99.78
3.08-3.880.18511440.162728598X-RAY DIFFRACTION99.63
3.88-34.360.15981470.154528942X-RAY DIFFRACTION99.1

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