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- PDB-6bbr: Room temperature neutron/X-ray structure of AAC-VIa -

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Basic information

Entry
Database: PDB / ID: 6bbr
TitleRoom temperature neutron/X-ray structure of 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 / DEUTERATED WATER / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.002 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 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Sep 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 1.3Oct 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint7 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.600, 86.100, 78.800
Angle α, β, γ (deg.)90.000, 94.000, 90.000
Int Tables number5
Space group name H-MI121
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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 15-18% PEG8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
ROTATING ANODERIGAKU MICROMAX-00322.0-4.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEAug 1, 2017
ORNL ANGER CAMERA2DIFFRACTOMETERAug 1, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
221
341
Reflection

Biso Wilson estimate: 38.7 Å2 / Entry-ID: 6BBR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)
2-502233697.43.40.0590.0370.071.245119.7
2.3-151280083.82.40.16727.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.073.40.48921710.8340.3110.5821.53895.3
2.07-2.153.50.39121980.8880.2440.4621.66195.6
2.15-2.253.40.28521730.9260.180.3381.62196.2
2.25-2.373.50.20322190.9550.1280.2411.75596.8
2.37-2.523.50.15322210.9780.0960.1811.42297
2.52-2.713.50.10822410.9860.0680.1281.35697.9
2.71-2.993.50.07922380.9910.0490.0931.15698.1
2.99-3.423.50.05722700.9920.0360.0670.90798.7
3.42-4.313.40.04522920.9920.0290.0540.62899.2
4.31-503.30.04223130.9930.0270.050.45499.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
Refinement

SU ML: 0.21 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 23.38 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: PDB entry 6BC6

6bc6

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
2.002-30.944X-RAY DIFFRACTION152.5454.619929.020.18890.15820.15981126223365.0496.3211.34
2.3-15NEUTRON DIFFRACTION0.24580.22060.222708140295.0589.3920
Refinement stepCycle: final / Resolution: 2.002→30.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 1 207 2236
Biso mean--53.76 57.53 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014651
X-RAY DIFFRACTIONf_angle_d0.9348185
X-RAY DIFFRACTIONf_chiral_restr0.065307
X-RAY DIFFRACTIONf_plane_restr0.005914
X-RAY DIFFRACTIONf_dihedral_angle_d20.5931235
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
2.0022-2.09330.31661230.25722394X-RAY DIFFRACTION2517887
2.0933-2.20370.24921330.22212618X-RAY DIFFRACTION2751896
2.2037-2.34170.2271540.19142638X-RAY DIFFRACTION2792897
2.3417-2.52240.22631310.19362651X-RAY DIFFRACTION2782897
2.5224-2.77610.21041490.18342675X-RAY DIFFRACTION2824898
2.7761-3.17750.22921410.18852717X-RAY DIFFRACTION2858898
3.1775-4.00190.18271460.14592735X-RAY DIFFRACTION2881899
4.0019-30.94780.14421490.12132782X-RAY DIFFRACTION2931899
2.2803-2.45570.39461190.36642267NEUTRON DIFFRACTION2386576
2.4557-2.70180.33391430.33242682NEUTRON DIFFRACTION2825590
2.7018-3.09010.29541460.26952724NEUTRON DIFFRACTION2870592
3.0901-3.88350.24411520.2222847NEUTRON DIFFRACTION2999596
3.8835-15.72770.20021480.1622801NEUTRON DIFFRACTION2949593

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