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- PDB-7csj: Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smeg... -

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Basic information

Entry
Database: PDB / ID: 7csj
TitleAminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Gentamicin
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / aminoglycoside acetyltransferase / antibiotics / gentamicin
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
gentamicin C1 / COENZYME A / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.168 Å
AuthorsJeong, C.S. / Hwang, J. / Do, H. / Lee, J.H.
CitationJournal: Sci Rep / Year: 2020
Title: Structural and biochemical analyses of an aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis.
Authors: Jeong, C.S. / Hwang, J. / Do, H. / Cha, S.S. / Oh, T.J. / Kim, H.J. / Park, H.H. / Lee, J.H.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Aminoglycoside 2'-N-acetyltransferase
B: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4105
Polymers46,3982
Non-polymers2,0133
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-10 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.486, 60.212, 116.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminoglycoside 2'-N-acetyltransferase / AAC(2')-Id


Mass: 23198.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: aac, MSMEG_0434, MSMEI_0423 / Production host: Escherichia coli (E. coli)
References: UniProt: P94968, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-51G / gentamicin C1 / (1S,2S,3R,4S,6R)-4,6-diamino-3-({(2R,3R,6S)-3-amino-6-[(1R)-1-(methylamino)ethyl]tetrahydro-2H-pyran-2-yl}oxy)-2-hydrox ycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside


Mass: 477.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H43N5O7
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate: citric acid (pH 5.5), 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.168→50 Å / Num. obs: 20679 / % possible obs: 97.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 37.985
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 791 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CRM

7crm


Resolution: 2.168→41.95 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1005 4.87 %RANDOM
Rwork0.1987 ---
obs0.201 20629 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.168→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 129 113 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163061
X-RAY DIFFRACTIONf_angle_d1.3314184
X-RAY DIFFRACTIONf_dihedral_angle_d7.0171772
X-RAY DIFFRACTIONf_chiral_restr0.106463
X-RAY DIFFRACTIONf_plane_restr0.006532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1681-2.28240.31861180.23412676X-RAY DIFFRACTION95
2.2824-2.42540.30161400.22992736X-RAY DIFFRACTION97
2.4254-2.61260.27581350.23192785X-RAY DIFFRACTION98
2.6126-2.87550.32251430.23532796X-RAY DIFFRACTION98
2.8755-3.29140.27531710.22222785X-RAY DIFFRACTION99
3.2914-4.14630.24221400.18192848X-RAY DIFFRACTION99

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