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- PDB-6ntj: Neutron/X-ray crystal structure of AAC-VIa bound to gentamicin C1A -

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Basic information

Entry
Database: PDB / ID: 6ntj
TitleNeutron/X-ray crystal structure of AAC-VIa bound to gentamicin C1A
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-LLL / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesEnterobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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)32,8043
Polymers32,3301
Non-polymers4742
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.319, 86.228, 51.003
Angle α, β, γ (deg.)90.000, 120.400, 90.000
Int Tables number5
Space group name H-MC121
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 K-12 (bacteria) / Strain (production host): K-12
References: UniProt: C4NV15, aminoglycoside 3-N-acetyltransferase
#2: Chemical ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H39N5O7 / Feature type: SUBJECT OF INVESTIGATION
#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 / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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 (PEG) 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, 2018
ORNL ANGER CAMERA2AREA DETECTORJan 1, 2018
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: 34.34 Å2 / Entry-ID: 6NTJ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)CC1/2
1.9-502600298.42.80.0560.0390.0681.456118.8
2.35-16.81067776.92.60.1170.0850.146280.989
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Diffraction-ID% possible all
1.9-1.972.60.65824440.6710.4840.8221.624193.3
1.97-2.052.80.51826200.7260.3790.6461.677199.5
2.05-2.142.80.3626310.850.260.4471.701199.2
2.14-2.252.80.2625590.9060.1860.3221.732199
2.25-2.392.80.17626430.9510.1260.2171.685198.9
2.39-2.582.80.12725960.9770.0910.1571.665198.7
2.58-2.842.80.08326150.9880.0590.1031.5198.9
2.84-3.252.90.05226100.9950.0370.0641.244198.9
3.25-4.092.90.03526270.9970.0240.0430.957199.2
4.09-5030.03726570.9960.0250.0450.927198.4
2.35-2.482.50.2912140.204259.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
Refinement

SU ML: 0.25 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 24.32 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 6bbz

6bbz

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)
1.9-43.114X-RAY DIFFRACTION157.7954.98729.490.19970.15660.15881304259965.0298.2711.34
2.35-16.8NEUTRON DIFFRACTION0.30920.26480.2671535106755.0176.0820
Refinement stepCycle: final / Resolution: 1.9→43.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 77 452 2551
Biso mean--51.52 64.9 -
Num. residues----267
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 (%)
2.3438-2.57890.44731040.41271971NEUTRON DIFFRACTION2075459
2.5789-2.95040.42881170.35052310NEUTRON DIFFRACTION2427470
2.9504-3.71060.31591510.2512746NEUTRON DIFFRACTION2897483
3.7106-16.82950.20721630.1793113NEUTRON DIFFRACTION3276492
1.896-1.97190.37811300.31192559X-RAY DIFFRACTION2689993
1.9719-2.06170.31691500.26392766X-RAY DIFFRACTION2916999
2.0617-2.17030.23721420.22512755X-RAY DIFFRACTION2897999
2.1703-2.30630.25961550.2032755X-RAY DIFFRACTION2910999
2.3063-2.48440.23471370.19122763X-RAY DIFFRACTION2900999
2.4844-2.73430.22571440.17922741X-RAY DIFFRACTION2885999
2.7343-3.12990.23661460.1742778X-RAY DIFFRACTION2924999
3.1299-3.94290.1931560.13622766X-RAY DIFFRACTION2922999
3.9429-43.12510.13741440.10732809X-RAY DIFFRACTION2953998

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