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- PDB-1m4d: Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 1m4d
TitleAminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis-Complex with Coenzyme A and Tobramycin
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / COA BINDING MOTIF
Function / homology
Function and homology information


aminoglycoside 2'-N-acetyltransferase activity / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / plasma membrane
Similarity search - Function
Acetyltransferase (GNAT) domain / 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 / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / TOBRAMYCIN / Aminoglycoside 2'-N-acetyltransferase / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S. / Roderick, S.L.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Aminoglycoside 2'-N-acetyltransferase from Mycobacterium tuberculosis in complex with coenzyme A and aminoglycoside substrates.
Authors: Vetting, M.W. / Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S. / Roderick, S.L.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Overexpression and Mechanistic Analysis of Chromosomally Encoded Aminoglycoside 2'-N-Acetyltransferase (AAC(2')-Ic) from Mycobacterium tuberculosis
Authors: Hegde, S.S. / Javid-Majd, F. / Blanchard, J.S.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,1057
Polymers40,1272
Non-polymers2,9775
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-25 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 86.600, 98.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer, as contained in the assymetric unit

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Components

#1: Protein Aminoglycoside 2'-N-acetyltransferase / Aminosugar N-Acetyltransferase / AAC(2')-IC


Mass: 20063.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5N0, UniProt: P9WQG9*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, ADA, Coenzyme A, Tobramycin, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMCoA11
220 mMaminoglycoside11
3100 mMADA11pH6.5
40.8 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2001 / Details: Confocal Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 39334 / Num. obs: 38420 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.036 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 4294 / Rsym value: 0.238 / % possible all: 93.8
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.238

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M44

1m44


Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1922 5 %random
Rwork0.174 ---
all0.174 38420 --
obs0.174 38420 97.7 %-
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 191 236 3210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.105
X-RAY DIFFRACTIONc_bond_d0.0237
LS refinement shellResolution: 1.8→1.88 Å
RfactorNum. reflection% reflection
Rfree0.261 231 -
Rwork0.241 --
obs-4538 92 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.174 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / Rfactor Rwork: 0.241

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