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- PDB-6bc3: Cryo X-ray structure of sisomicin bound AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bc3
TitleCryo X-ray structure of sisomicin bound AAC-VIa
ComponentsAAC 3-VI protein
KeywordsTRANSFERASE/ANTIBIOTIC / acetyltransferase / 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
COENZYME A / Chem-SIS / Aminoglycoside N(3)-acetyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsCuneo, M.J. / Kumar, P. / Serpersu, E.H.
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)33,5603
Polymers32,3441
Non-polymers1,2152
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-0 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.534, 77.534, 83.890
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, pH 5.6, 0.2 M ammonium acetate, 10% glycerol, 17-25% PEG4000

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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: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.047→50 Å / Num. obs: 18004 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.58 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.38 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.122.70.60217671.439198.2
2.12-2.212.80.49617911.567199
2.21-2.312.80.40817731.637199
2.31-2.432.80.34117921.655198.8
2.43-2.582.90.25517861.623199.1
2.58-2.782.90.218031.658199.8
2.78-3.0630.14217971.354199.8
3.06-3.5130.09118161.145199.9
3.51-4.4230.06218370.9351100
4.42-5030.05518420.922199.2

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BC6

6bc6


Resolution: 2.047→38.767 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 899 5 %
Rwork0.1893 --
obs0.1902 17988 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.047→38.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 79 187 2294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022192
X-RAY DIFFRACTIONf_angle_d0.633012
X-RAY DIFFRACTIONf_dihedral_angle_d20.863774
X-RAY DIFFRACTIONf_chiral_restr0.042326
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0469-2.17520.26791480.27722815X-RAY DIFFRACTION98
2.1752-2.34310.25111510.2432810X-RAY DIFFRACTION99
2.3431-2.57880.27431420.22842847X-RAY DIFFRACTION99
2.5788-2.95190.25811530.21222836X-RAY DIFFRACTION100
2.9519-3.71860.20021500.18532879X-RAY DIFFRACTION100
3.7186-38.77390.15361550.14592902X-RAY DIFFRACTION100

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