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

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Basic information

Entry
Database: PDB / ID: 7crm
TitleAminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-APO Structure
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / aminoglycoside acetyltransferase / antibiotics
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / response to antibiotic / Aminoglycoside 2'-N-acetyltransferase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.487 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 13, 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
C: Aminoglycoside 2'-N-acetyltransferase
D: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0448
Polymers92,7954
Non-polymers2484
Water2,468137
1
A: Aminoglycoside 2'-N-acetyltransferase
B: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5224
Polymers46,3982
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-7 kcal/mol
Surface area16830 Å2
MethodPISA
2
C: Aminoglycoside 2'-N-acetyltransferase
D: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5224
Polymers46,3982
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-7 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.008, 81.212, 129.768
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.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. obs: 26178 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 31.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.475 / Num. unique obs: 1297 / % possible all: 100

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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: 1M44

1m44


Resolution: 2.487→34.421 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1267 4.85 %
Rwork0.193 --
obs0.1968 26122 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.487→34.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 16 137 5949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075839
X-RAY DIFFRACTIONf_angle_d0.9487936
X-RAY DIFFRACTIONf_dihedral_angle_d3.4993423
X-RAY DIFFRACTIONf_chiral_restr0.05876
X-RAY DIFFRACTIONf_plane_restr0.0051047
LS refinement shellResolution: 2.487→2.5865 Å
RfactorNum. reflection% reflection
Rfree0.3565 147 -
Rwork0.2426 2582 -
obs--95 %

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