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- PDB-6bc4: Cryo X-ray structure of acetyl coenzyme A bound AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bc4
TitleCryo X-ray structure of acetyl coenzyme A bound AAC-VIa
ComponentsAAC 3-VI protein
KeywordsTRANSFERASE / acetyltransferase
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / metal ion binding / ACETYL COENZYME *A / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.049 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)33,1542
Polymers32,3441
Non-polymers8101
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-2 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.515, 78.515, 83.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
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: 2.049→50 Å / Num. obs: 18240 / % possible obs: 98.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 23.02 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.316 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.122.10.52618011.433197
2.12-2.212.50.44418301.473199.6
2.21-2.312.60.3618171.457199.1
2.31-2.432.60.31318101.461199.3
2.43-2.582.60.23918241.434199.4
2.58-2.782.60.17218441.367199.5
2.78-3.062.60.1318151.324199.2
3.06-3.512.60.07618451.199199.1
3.51-4.422.70.04518471.026198.6
4.42-502.70.03618071.068195.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BC6

6bc6


Resolution: 2.049→35.555 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.2047 905 4.96 %
Rwork0.1789 --
obs0.1802 18236 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.41 Å2 / Biso mean: 22.7012 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 2.049→35.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 51 274 2353
Biso mean--31.62 29.05 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022156
X-RAY DIFFRACTIONf_angle_d0.5672958
X-RAY DIFFRACTIONf_chiral_restr0.042314
X-RAY DIFFRACTIONf_plane_restr0.004389
X-RAY DIFFRACTIONf_dihedral_angle_d5.2931709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0493-2.17770.29971480.26222839298797
2.1777-2.34580.2591470.22372901304899
2.3458-2.58180.2261510.20652880303199
2.5818-2.95520.24581490.19312911306099
2.9552-3.72270.19781540.16062922307699
3.7227-35.55980.14541560.13922878303497

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