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- PDB-6bc6: Cryo X-ray structure of apo AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bc6
TitleCryo X-ray structure of apo 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 / 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.
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 / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
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 ...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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)32,3692
Polymers32,3441
Non-polymers241
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area12430 Å2
Unit cell
Length a, b, c (Å)89.010, 85.981, 51.134
Angle α, β, γ (deg.)90.000, 119.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 15-20% PEG8000, 0.3 M magnesium chloride

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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, 2016
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: 15393 / % possible obs: 90.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 37.38 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.451 / Net I/σ(I): 18.4 / Num. measured all: 37319
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.282.20.50415971.616194.7
2.28-2.372.30.41815881.766194.5
2.37-2.482.30.36416141.73193.5
2.48-2.612.40.27115431.695192.7
2.61-2.772.40.18715561.707192
2.77-2.992.40.13815561.649191.1
2.99-3.292.50.09815221.573190
3.29-3.762.50.06815061.32188.6
3.76-4.742.60.06114860.904186.5
4.74-502.70.05714250.724182.1

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SMA

3sma


Resolution: 2.2→30.849 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2
RfactorNum. reflection% reflection
Rfree0.2673 771 5.01 %
Rwork0.2364 --
obs0.238 15388 90.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.63 Å2 / Biso mean: 43.9968 Å2 / Biso min: 23.09 Å2
Refinement stepCycle: final / Resolution: 2.2→30.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 1 51 2080
Biso mean--43.2 42.23 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022086
X-RAY DIFFRACTIONf_angle_d0.4822853
X-RAY DIFFRACTIONf_chiral_restr0.041307
X-RAY DIFFRACTIONf_plane_restr0.006380
X-RAY DIFFRACTIONf_dihedral_angle_d7.6391237
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 (%)
2.1982-2.33580.33251340.31392502263693
2.3358-2.51610.31061340.3022502263694
2.5161-2.76920.32891300.29152468259892
2.7692-3.16950.32211340.27652435256991
3.1695-3.99190.29691180.21592411252989
3.9919-30.85210.18671210.19082299242084

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