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- PDB-6nti: Neutron/X-ray crystal structure of AAC-VIa bound to kanamycin b -

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Basic information

Entry
Database: PDB / ID: 6nti
TitleNeutron/X-ray crystal structure of AAC-VIa bound to kanamycin b
ComponentsAminoglycoside N(3)-acetyltransferase
Keywordstransferase/antibiotic / acetyl transferase / neutron / TRANSFERASE / transferase-antibiotic complex
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 / Chem-9CS / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCuneo, M.J. / Kumar, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.
Authors: Kumar, P. / Agarwal, P.K. / Waddell, M.B. / Mittag, T. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8383
Polymers32,3301
Non-polymers5082
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.359, 86.058, 77.597
Angle α, β, γ (deg.)90.00, 93.98, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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Components

#1: Protein Aminoglycoside N(3)-acetyltransferase


Mass: 32330.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteriaceae (bacteria)
Gene: aacC, aac3-VI, aac3-VI_1, NCTC13462_00209, pAPEC1990_61_126, pAR060302_0140, pAR060302_133, peH4H_0115, SAMEA3485113_05325
Production host: Escherichia coli DH1 (bacteria)
References: UniProt: C4NV15, aminoglycoside 3-N-acetyltransferase
#2: Chemical ChemComp-9CS / (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE / Kanamycin B / Bekanamycin


Mass: 483.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O10 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: polyethylene glycol 8000, 0.2 M MgCl2, 0.1 M Tris, pH 8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
NUCLEAR REACTORORNL Spallation Neutron Source MANDI22.0-4.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJan 1, 2017
ORNL ANGER CAMERA2AREA DETECTORJan 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

Entry-ID: 6NTI

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.3-501395593.430.061114.7
2.3-14.081296985.22.60.14827.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.382.90.3473.34190
2.3-2.381.930.2442.8270.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 6BBZ

6bbz

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLR Free selection detailsCross valid methodσ(F)Phase errorShrinkage radii (Å)VDW probe radii (Å)Details
2.3-14X-RAY DIFFRACTION53.270.2570.2370.238638128594.96860.22RandomTHROUGHOUT022.180.91.11NEUTRON DATA.
NEUTRON DIFFRACTION
Refinement stepCycle: LAST / Resolution: 2.3→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 34 70 2131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2978-2.47510.26461290.22942547X-RAY DIFFRACTION90
2.3001-2.47670.39771090.3752268X-RAY DIFFRACTION80
2.4751-2.72410.23441360.21012597X-RAY DIFFRACTION91
2.4767-2.72430.34781310.34522331X-RAY DIFFRACTION83
2.7241-3.11790.23931420.20172674X-RAY DIFFRACTION94
2.7243-3.11480.30091240.30122435X-RAY DIFFRACTION86
3.1148-3.91010.23321340.23042595X-RAY DIFFRACTION91
3.1179-3.9270.17951400.15642734X-RAY DIFFRACTION95
3.9101-14.00150.20151400.16072592X-RAY DIFFRACTION90
3.927-30.82080.14851500.12192793X-RAY DIFFRACTION96

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