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- PDB-6o5u: AAC-VIa bound to Kanamycin A -

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Basic information

Entry
Database: PDB / ID: 6o5u
TitleAAC-VIa bound to Kanamycin A
ComponentsAminoglycoside N(3)-acetyltransferase
Keywordstransferase/antibiotic / Antibiotic modifying enzyme / substrate selectivity / ANTIBIOTIC / TRANSFERASE / transferase-antibiotic complex
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 / KANAMYCIN A / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacteriaceae (enterobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionMar 4, 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)32,8393
Polymers32,3301
Non-polymers5092
Water7,170398
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)87.271, 86.282, 50.193
Angle α, β, γ (deg.)90.000, 119.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-781-

HOH

31A-796-

HOH

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Components

#1: Protein Aminoglycoside N(3)-acetyltransferase


Mass: 32330.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteriaceae (enterobacteria) / Gene: aac 3-VI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q47030, aminoglycoside 3-N-acetyltransferase
#2: Chemical ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N4O11 / Feature type: SUBJECT OF INVESTIGATION / 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.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / Details: 15-20% PEG 8000, 0.1M Tris pH 8.5 and 0.3M 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: 1.394→50 Å / Num. obs: 63478 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.79 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 0.621 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4330.3842080.8910.2580.4610.44399.4
1.43-1.473.20.33441810.9140.2190.4010.4698.7
1.47-1.513.20.25441800.9520.1660.3040.46899.3
1.51-1.553.50.20442150.970.1280.2410.4799.3
1.55-1.63.50.17441710.9760.1090.2060.50198.3
1.6-1.663.50.13142180.9850.0830.1550.49999.2
1.66-1.733.40.10542410.9890.0670.1250.599.6
1.73-1.83.20.08642290.990.0570.1040.53199.8
1.8-1.93.30.0742300.9930.0450.0830.53799.8
1.9-2.023.50.05842490.9940.0370.0690.58199.9
2.02-2.183.50.04942590.9960.030.0580.599100
2.18-2.393.50.04542560.9950.0290.0540.681100
2.39-2.743.20.04242530.9950.0280.0510.772100
2.74-3.453.50.03742770.9970.0230.0430.86999.9
3.45-503.40.03343110.9970.0220.041.35299.5

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Processing

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

6bbz


Resolution: 1.4→40.129 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1558 3179 5.01 %
Rwork0.1286 --
obs0.13 63461 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.69 Å2 / Biso mean: 26.5401 Å2 / Biso min: 12.84 Å2
Refinement stepCycle: final / Resolution: 1.4→40.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 139 398 2564
Biso mean--22.89 40.71 -
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 (%)
1.4-1.41440.24411250.2457228689
1.4144-1.43650.25071480.2299262298
1.4365-1.46010.27761370.2041260199
1.4601-1.48530.19161250.187262299
1.4853-1.51230.17341430.16392616100
1.5123-1.54140.20831490.1517259299
1.5414-1.57280.16791390.1448262599
1.5728-1.6070.16941320.1391260398
1.607-1.64440.16911340.134261999
1.6444-1.68550.16881400.13092631100
1.6855-1.73110.15471420.12692634100
1.7311-1.7820.151370.12692632100
1.782-1.83960.15261330.12312632100
1.8396-1.90530.15391530.12492625100
1.9053-1.98160.14161310.11792660100
1.9816-2.07180.14871340.12442652100
2.0718-2.1810.13691400.12172656100
2.181-2.31760.13251440.11392622100
2.3176-2.49650.13351400.11422673100
2.4965-2.74770.13671320.11892644100
2.7477-3.14520.16651400.12362684100
3.1452-3.96210.15561410.12192660100
3.9621-40.1290.15471400.131269199

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