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- PDB-2vbq: Structure of AAC(6')-Iy in complex with bisubstrate analog CoA-S-... -

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Basic information

Entry
Database: PDB / ID: 2vbq
TitleStructure of AAC(6')-Iy in complex with bisubstrate analog CoA-S- monomethyl-acetylneamine.
ComponentsAMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / AMINOGLYCOSIDE / ACETYLTRANSFERASE / DRUG RESISTANCE / BISUBSTRATE INHIBITOR
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
Chem-BSJ / NICKEL (II) ION / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesSALMONELLA CHOLERAESUIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVetting, M.W. / Magalhaes, M.L. / Freiburger, L. / Gao, F. / Auclair, K. / Blanchard, J.S.
CitationJournal: Biochemistry / Year: 2008
Title: Kinetic and Structural Analysis of Bisubstrate Inhibition of the Salmonella Enterica Aminoglycoside 6'-N-Acetyltransferase.
Authors: Magalhaes, M.L. / Vetting, M.W. / Gao, F. / Freiburger, L. / Auclair, K. / Blanchard, J.S.
History
DepositionSep 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Mar 11, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.6May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)39,5486
Polymers37,1142
Non-polymers2,4354
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-51 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.964, 44.599, 88.387
Angle α, β, γ (deg.)90.00, 93.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE / AMINOGLYCOSIDE ACETYLTRANSFERASE IY


Mass: 18556.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA CHOLERAESUIS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9R381, aminoglycoside 6'-N-acetyltransferase
#2: Chemical ChemComp-BSJ / (3R,9Z)-17-[(2R,3S,4R,5R,6R)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]-3-hydroxy-2,2-dimethyl-4,8,15-trioxo-12-thia-5,9,16-triazaheptadec-9-en-1-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 1141.924 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H62N11O23P3S
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-(BIPHENYL-4-SULFONYL)-1,2,3, 4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (BSJ): COA-S-MONOMETHYL- ...2-(BIPHENYL-4-SULFONYL)-1,2,3, 4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (BSJ): COA-S-MONOMETHYL-ACETYLNEAMINE COENZYMEA COVALENTLY LINKED TO N-ACETYLNEAMINE THROUGH A METHYL LINKER NOVEL HETROGEN REQUIRES NEW HET CODE
Sequence detailsPROTEIN CONTAINS N-TERMINAL TAG

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 5.75
Details: PROTEIN (15MG/ML, 10 MM TEA PH 8.0, 100 MM AMMONIUM SULFATE), PRECIPITANT (20 % PEG6000, 100 MM MES PH 5.75) VAPOUR DIFFUSION UNDER OIL

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Details: CONFOCAL BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 21649 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.5 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→88.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.702 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL THROMBIN CLEAVABLE 6X-HIS TAG CLEAVED PRIOR TO CRYSTALLIZATION (PET28 ORIGIN).
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1102 5.1 %RANDOM
Rwork0.181 ---
obs0.183 20546 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-1.19 Å2
2---0.56 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→88.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 155 219 2684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222524
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.56223428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13823.252123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49815397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0061522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021896
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21670
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.971.51497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5822308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32631175
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6074.51120
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 87
Rwork0.221 1365

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