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- PDB-1s3z: Aminoglycoside N-Acetyltransferase AAC(6')-Iy in Complex with CoA... -

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Basic information

Entry
Database: PDB / ID: 1s3z
TitleAminoglycoside N-Acetyltransferase AAC(6')-Iy in Complex with CoA and Ribostamycin
Componentsaminoglycoside 6'-N-acetyltransferase
KeywordsTRANSFERASE / GNAT / N-acetyltransferase / acetyltransferase / aminoglycoside / CoA / ribostamycin
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / 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 / NICKEL (II) ION / RIBOSTAMYCIN / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesSalmonella enteritidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Magnet, S. / Nieves, E. / Roderick, S.L. / Blachard, 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. / Blachard, 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.S.
History
DepositionJan 14, 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: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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 6'-N-acetyltransferase
B: aminoglycoside 6'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8099
Polymers37,1142
Non-polymers2,6957
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-61 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.989, 44.688, 87.974
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-829-

HOH

DetailsThe biological assembly is a dimer as generated from the dimer in the assymetric unit by the operations x,y,z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 18556.926 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 454.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34N4O10 / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / pH: 8
Details: Peg 3350, ammonium sulfate, triethanolamine, coenzyme A, ribostamycin, pH 8.0, vapor diffusion under oil, temperature 293K, pH 8.00

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2002 / Details: MSC BLUE CONFOCAL
RadiationMonochromator: MSC BLUE CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20976 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.053 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.152 / % possible all: 67.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.21 1011 RANDOM
Rwork0.167 --
obs0.167 20954 -
all-20954 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 169 217 2704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.178

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