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- PDB-1s60: Aminoglycoside N-Acetyltransferase AAC(6')-Iy in Complex with CoA... -

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Basic information

Entry
Database: PDB / ID: 1s60
TitleAminoglycoside N-Acetyltransferase AAC(6')-Iy in Complex with CoA and N-terminal His(6)-tag (crystal form 2)
Componentsaminoglycoside 6'-N-acetyltransferase
KeywordsTRANSFERASE / GNAT / N-acetyltransferase / acetyltransferase / aminoglycoside / CoA
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase activity / aminoglycoside 6'-N-acetyltransferase / acetyl-CoA metabolic process / response to antibiotic / protein homodimerization activity
Similarity search - Function
Aminoglycoside N6-acetyltransferase / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesSalmonella enteritidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVetting, M.W. / Magnet, S. / Nieves, E. / Roderick, S.L. / Blanchard, J.S.
Citation
Journal: Chem.Biol. / Year: 2004
Title: A bacterial acetyltransferase capable of regioselective N-acetylation of antibiotics and histones
Authors: Vetting, M.W. / Magnet, S. / Nieves, E. / Roderick, S.L. / Blanchard, J.S.
#1: Journal: Biochemistry / Year: 2001
Title: Kinetic and mutagenic characterization of the chromosomally encoded Salmonella enterica AAC(6')-Iy aminoglycoside N-acetyltransferase
Authors: Magnet, S. / Lambert, T. / Courvalin, P. / Blanchard, J.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aminoglycoside 6'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4213
Polymers18,5571
Non-polymers8642
Water00
1
A: aminoglycoside 6'-N-acetyltransferase
hetero molecules

A: aminoglycoside 6'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8416
Polymers37,1142
Non-polymers1,7274
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+4/31
Buried area6890 Å2
ΔGint-53 kcal/mol
Surface area15720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.600, 84.600, 66.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer generated from the monomer in the assymetric unit by the operations 1 0 0 0 -1 0 0 0 -1 0 146.5 89.0

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Components

#1: Protein aminoglycoside 6'-N-acetyltransferase / Aminoglycoside N-Acetyltransferase AAC(6')-Iy


Mass: 18556.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enteritidis (bacteria) / Plasmid: pet28a+ / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R381, aminoglycoside 6'-N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / 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: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion under oil / pH: 8.8
Details: Bicine, Ammonium Sulfate, pH 8.8, vapor diffusion under oil, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 26, 2002 / Details: MSC Blue Confocal
RadiationMonochromator: Optics MSC Blue Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 5773 / Num. obs: 5773 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 71 Å2 / Rsym value: 0.046 / Net I/σ(I): 19.8
Reflection shellResolution: 3→3.11 Å / Rsym value: 0.136 / % possible all: 87

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Partially refined model created by fitting a Se-MET derived Map from same crystal form collected at synchotron radiation source.

Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 306 -random
Rwork0.225 ---
obs0.225 5559 95.9 %-
all-5559 --
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 53 0 1253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.95
X-RAY DIFFRACTIONc_bond_d0.0148
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree: 0.352 / Rfactor Rwork: 0.281

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