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- PDB-6np1: Product state mimicry leads to aminoglycoside discrimination in a... -

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Basic information

Entry
Database: PDB / ID: 6np1
TitleProduct state mimicry leads to aminoglycoside discrimination in an antibiotic acetyltransferase
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 / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7833
Polymers28,7341
Non-polymers492
Water3,729207
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)85.349, 86.576, 50.352
Angle α, β, γ (deg.)90.000, 118.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-520-

HOH

21A-607-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
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: 1.6→50 Å / Num. obs: 41106 / % possible obs: 97.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.15 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.06 / Rrim(I) all: 0.109 / Χ2: 1.987 / Net I/σ(I): 11.3 / Num. measured all: 133616
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.643.30.31128110.9020.2010.3711.27799.9
1.64-1.683.30.26627680.9360.1710.3171.483100
1.68-1.723.30.23327800.9440.1470.2761.65499.9
1.72-1.773.20.20927950.9430.1350.2491.99599.9
1.77-1.833.10.18527610.9480.1230.2232.49699.6
1.83-1.93.20.17228360.9490.1110.2052.26699.8
1.9-1.973.30.15127880.9650.0970.1793.08799.9
1.97-2.063.50.13527820.9760.0840.1591.72499.9
2.06-2.173.40.13328090.9770.0830.1572.024100
2.17-2.313.40.11827820.980.0750.142.18799.8
2.31-2.493.30.10927970.9810.0710.132.13999.6
2.49-2.7430.10327660.980.0690.1242.08798.5
2.74-3.133.20.09126390.9840.060.1092.12693.9
3.13-3.953.20.08324860.9860.0550.11.9487.9
3.95-5030.07325060.9840.050.0891.25587.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BC6

6bc6


Resolution: 1.6→43.287 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.74
RfactorNum. reflection% reflection
Rfree0.2379 1997 4.86 %
Rwork0.2069 --
obs0.2085 41077 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.91 Å2 / Biso mean: 37.2544 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: final / Resolution: 1.6→43.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 2 207 2236
Biso mean--37.36 41.63 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122121
X-RAY DIFFRACTIONf_angle_d1.152906
X-RAY DIFFRACTIONf_chiral_restr0.075310
X-RAY DIFFRACTIONf_plane_restr0.009391
X-RAY DIFFRACTIONf_dihedral_angle_d5.4341706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63770.31071310.30292566269789
1.6377-1.6820.2981440.28228412985100
1.682-1.73150.30311470.255728743021100
1.7315-1.78740.28771480.244628883036100
1.7874-1.85130.30251450.23852835298099
1.8513-1.92540.25711450.2328402985100
1.9254-2.0130.23831490.226729083057100
2.013-2.11920.24921450.205828352980100
2.1192-2.25190.24741470.214128843031100
2.2519-2.42580.23461460.202828723018100
2.4258-2.66990.26761460.20872851299799
2.6699-3.05610.22721420.20912760290295
3.0561-3.850.22091310.20332563269489
3.85-43.30330.21521310.17992563269487

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