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- PDB-6bc7: Cryo X-ray structure of sisomicin bound AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bc7
TitleCryo X-ray structure of sisomicin bound AAC-VIa
ComponentsAAC 3-VI protein
KeywordsTRANSFERASE/ANTIBIOTIC / acetyltransferase / sisomicin / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


aminoglycoside 3-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / metal ion binding
Similarity search - Function
Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like
Similarity search - Domain/homology
ACETATE ION / Chem-SIS / Aminoglycoside N(3)-acetyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCuneo, M.J. / Kumar, P.
CitationJournal: Sci Adv / Year: 2018
Title: A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad.
Authors: Kumar, P. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAC 3-VI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8513
Polymers32,3441
Non-polymers5072
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.550, 78.550, 83.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein AAC 3-VI protein / AAC-VIa


Mass: 32344.461 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 (E. coli) / References: UniProt: Q47030
#2: Chemical ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin


Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O7 / Comment: antibiotic*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 17-25% PEG4000, 0.1 M sodium citrate, pH 5.6, 0.2 M ammonium acetate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26880 / % possible obs: 98.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.54 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.258 / Net I/σ(I): 9.1 / Num. measured all: 76779
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.852.80.53221901.332196.3
1.85-1.912.80.4522091.403197.5
1.91-1.982.80.33421861.413197.7
1.98-2.062.80.26922091.432198.4
2.06-2.152.80.21822411.44198.5
2.15-2.272.80.17922291.455199.1
2.27-2.412.90.15422521.358199.4
2.41-2.62.90.12222621.289199.7
2.6-2.862.90.09222581.219199.8
2.86-3.272.90.06422771.138199.8
3.27-4.122.90.03922690.908199.2
4.12-502.90.03322980.767199

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BC6

6bc6


Resolution: 1.8→35.615 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1857 1303 4.85 %
Rwork0.1491 --
obs0.1508 26876 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 35 402 2465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092191
X-RAY DIFFRACTIONf_angle_d0.9873010
X-RAY DIFFRACTIONf_dihedral_angle_d21.421786
X-RAY DIFFRACTIONf_chiral_restr0.065328
X-RAY DIFFRACTIONf_plane_restr0.007399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7995-1.87160.29261730.22472737X-RAY DIFFRACTION97
1.8716-1.95680.24031640.20062769X-RAY DIFFRACTION98
1.9568-2.05990.20551290.16532816X-RAY DIFFRACTION98
2.0599-2.1890.20611230.15382879X-RAY DIFFRACTION99
2.189-2.35790.18471530.14782820X-RAY DIFFRACTION99
2.3579-2.59520.18211480.14772858X-RAY DIFFRACTION100
2.5952-2.97050.18431200.15082896X-RAY DIFFRACTION100
2.9705-3.74190.17511430.13492893X-RAY DIFFRACTION100
3.7419-35.62210.14491500.12762905X-RAY DIFFRACTION100

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