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- PDB-6np4: AAC-VIa bound to Tobramycin -

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Basic information

Entry
Database: PDB / ID: 6np4
TitleAAC-VIa bound to Tobramycin
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE / Antibiotic modifying enzyme / substrate selectivity / ANTIBIOTIC
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / metal ion binding / TOBRAMYCIN / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.151 Å
AuthorsKumar, P. / Cuneo, M.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.
Authors: Kumar, P. / Agarwal, P.K. / Waddell, M.B. / Mittag, T. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionJan 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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 / 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_asym_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_asym_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2263
Polymers28,7341
Non-polymers4922
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.642, 86.157, 50.241
Angle α, β, γ (deg.)90.000, 119.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-766-

HOH

31A-792-

HOH

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Components

#1: Protein Aminoglycoside N(3)-acetyltransferase


Mass: 28734.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: aac 3-VI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q47030, aminoglycoside 3-N-acetyltransferase
#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.: 1 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: 15-20% polyethylene glycol (PEG) 8000,0.1 M Tris, pH 8.5 and 0.3 M MgCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 114083 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.02 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Χ2: 0.672 / Net I/σ(I): 7.8 / Num. measured all: 383601
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.183.30.40375640.8820.2640.4840.45599.8
1.18-1.213.10.3476050.9090.2260.410.45699.9
1.21-1.243.30.28175580.9380.1820.3360.45399.8
1.24-1.283.20.23176220.9550.1510.2770.471100
1.28-1.323.50.19275880.970.1220.2280.474100
1.32-1.363.40.1676620.9770.1030.1910.493100
1.36-1.423.50.12775370.9840.0810.1510.506100
1.42-1.483.40.09976250.9890.0640.1180.53199.9
1.48-1.563.20.07575940.9920.0490.090.5999.9
1.56-1.663.40.06276170.9950.0390.0730.652100
1.66-1.793.60.05276110.9960.0320.0610.703100
1.79-1.973.50.04575940.9970.0280.0530.848100
1.97-2.253.30.04176430.9960.0270.0491.01899.9
2.25-2.843.50.03676320.9970.0230.0431.10899.8
2.84-503.30.03276310.9970.0210.0391.26498.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BC6

6bc6


Resolution: 1.151→43.273 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1394 5705 5 %
Rwork0.1247 108362 -
obs0.1255 114067 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.55 Å2 / Biso mean: 23.2815 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 1.151→43.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 139 418 2584
Biso mean--22.03 38.4 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.151-1.16380.23211860.2265353097
1.1638-1.17750.2261880.21383555100
1.1775-1.19180.21631900.1993626100
1.1918-1.20690.23531890.19183596100
1.2069-1.22280.19051890.18373583100
1.2228-1.23950.20331900.17013609100
1.2395-1.25720.17031930.16653654100
1.2572-1.2760.17931870.15033562100
1.276-1.2960.16961910.1433630100
1.296-1.31720.16081890.13953604100
1.3172-1.33990.15181920.13253641100
1.3399-1.36430.14661920.12713643100
1.3643-1.39050.13691890.11633580100
1.3905-1.41890.1251890.11433602100
1.4189-1.44980.13871890.10983589100
1.4498-1.48350.13181920.10323651100
1.4835-1.52060.12851890.09843592100
1.5206-1.56170.11191920.0983634100
1.5617-1.60770.11571900.0943623100
1.6077-1.65960.10711910.09363616100
1.6596-1.71890.11021890.09633599100
1.7189-1.78770.1041910.10113641100
1.7877-1.86910.11671920.10693639100
1.8691-1.96760.11941890.10763588100
1.9676-2.09090.12161920.11093641100
2.0909-2.25230.10951900.1143622100
2.2523-2.47890.13191920.11653652100
2.4789-2.83760.14611900.1243605100
2.8376-3.57480.14611920.1348363699
3.5748-43.2730.15831910.1399361998

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