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- PDB-6bc5: Cryo X-ray structure of coenzyme A bound AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bc5
TitleCryo X-ray structure of coenzyme A bound AAC-VIa
ComponentsAAC 3-VI protein
KeywordsTRANSFERASE / acetyltransferase
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 / COENZYME A / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: AAC 3-VI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1122
Polymers32,3441
Non-polymers7681
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-1 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.068, 78.068, 83.278
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-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
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: 2.2→50 Å / Num. obs: 14077 / % possible obs: 95.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.665 / Net I/σ(I): 12.5 / Num. measured all: 78425
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.264.90.4848771.663172.2
2.26-2.345.50.42711811.688195.2
2.34-2.425.60.37811671.645195.7
2.42-2.525.60.32111791.716195.9
2.52-2.635.70.2611711.79196.4
2.63-2.775.70.21612011.823196.9
2.77-2.955.60.1711961.75197.2
2.95-3.175.60.13111981.756197.7
3.17-3.495.60.09512041.665197.6
3.49-45.60.06612171.562198.4
4-5.045.60.04912251.42198.9
5.04-505.50.0412611.517198.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
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: 2.2→39.034 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.48
RfactorNum. reflection% reflection
Rfree0.2122 688 4.89 %
Rwork0.1765 --
obs0.1782 14074 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.85 Å2 / Biso mean: 33.4729 Å2 / Biso min: 20.58 Å2
Refinement stepCycle: final / Resolution: 2.2→39.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 48 129 2205
Biso mean--59.85 35.85 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022152
X-RAY DIFFRACTIONf_angle_d0.5832953
X-RAY DIFFRACTIONf_chiral_restr0.043315
X-RAY DIFFRACTIONf_plane_restr0.004387
X-RAY DIFFRACTIONf_dihedral_angle_d5.5081708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1985-2.36820.25751420.20492425256787
2.3682-2.60650.25331230.20422688281196
2.6065-2.98350.22841460.20142695284197
2.9835-3.75840.21041420.18022753289598
3.7584-39.04010.18651350.15192825296099

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