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- PDB-7mql: AAC(3)-IIIa in complex with CoA and neomycin -

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Basic information

Entry
Database: PDB / ID: 7mql
TitleAAC(3)-IIIa in complex with CoA and neomycin
ComponentsAminoglycoside N(3)-acetyltransferase III
KeywordsTRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase
Function / homology
Function and homology information


2-deoxystreptamine metabolic process / aminoglycoside 3-N-acetyltransferase / antibiotic metabolic process / aminoglycoside 3-N-acetyltransferase activity / acetyl-CoA catabolic process / coenzyme A binding / cellular response to antibiotic / protein homodimerization activity / identical protein binding
Similarity search - Function
Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like
Similarity search - Domain/homology
COENZYME A / FORMIC ACID / RIBOSTAMYCIN / Aminoglycoside N(3)-acetyltransferase III
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsZielinski, M. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Plos One / Year: 2022
Title: Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa.
Authors: Zielinski, M. / Blanchet, J. / Hailemariam, S. / Berghuis, A.M.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase III
B: Aminoglycoside N(3)-acetyltransferase III
C: Aminoglycoside N(3)-acetyltransferase III
D: Aminoglycoside N(3)-acetyltransferase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,04820
Polymers119,7924
Non-polymers5,25616
Water23,3471296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.584, 90.882, 100.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-635-

HOH

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Components

#1: Protein
Aminoglycoside N(3)-acetyltransferase III / ACC(3)-III / Aminocyclitol 3-N-acetyltransferase type III / Gentamicin-(3)-N-acetyl-transferase


Mass: 29947.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aacC3 / Production host: Escherichia coli (E. coli)
References: UniProt: P29808, aminoglycoside 3-N-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 454.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H34N4O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium formate, 21% (w/v) PEG 3350, 2% (v/v) 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.6→31.05 Å / Num. obs: 157232 / % possible obs: 99.81 % / Redundancy: 13.7 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 20.85
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 15589 / CC1/2: 0.604

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PROTEUM PLUS2018.7-2data reduction
PROTEUM PLUS2018.7-2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→31.05 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1644 1.05 %
Rwork0.1756 --
obs0.1759 157232 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7987 0 340 1296 9623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089149
X-RAY DIFFRACTIONf_angle_d1.05212594
X-RAY DIFFRACTIONf_dihedral_angle_d19.6451308
X-RAY DIFFRACTIONf_chiral_restr0.0611391
X-RAY DIFFRACTIONf_plane_restr0.0081591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.35111360.341712743X-RAY DIFFRACTION99
1.65-1.70.33021360.309112809X-RAY DIFFRACTION100
1.7-1.760.28431340.268212879X-RAY DIFFRACTION100
1.76-1.830.31471360.225612874X-RAY DIFFRACTION100
1.83-1.910.23191370.197212846X-RAY DIFFRACTION100
1.91-2.020.21411370.178812948X-RAY DIFFRACTION100
2.02-2.140.1951340.166112886X-RAY DIFFRACTION100
2.14-2.310.19161390.156612934X-RAY DIFFRACTION100
2.31-2.540.17321360.154612994X-RAY DIFFRACTION100
2.54-2.910.1991370.157113031X-RAY DIFFRACTION100
2.91-3.660.15951400.148213146X-RAY DIFFRACTION100
3.66-31.050.14731420.141513498X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5248-0.0927-0.04860.87940.42530.9783-0.1092-0.127-0.01320.44290.03550.10090.1683-0.00130.05220.26680.03390.01860.1402-0.01630.120920.833437.651260.9857
20.9069-0.38840.01991.1817-0.34191.97060.12350.1976-0.1353-0.391-0.15830.2584-0.1835-0.16010.03490.26330.0583-0.07120.1494-0.06050.159514.94146.938129.9767
30.5937-0.0009-0.03681.45210.27590.9816-0.0378-0.0262-0.02420.11660.00560.01280.03460.01880.05170.1051-0.00180.00340.0989-0.02020.100423.516934.609744.9414
40.3334-0.18860.08913.1951-0.22711.29980.01830.01650.0091-0.0073-0.04050.071-0.13150.02390.06710.1532-0.01470.02250.1279-0.03980.120721.176734.213528.12
50.1763-0.1385-0.29560.15430.19160.78450.02-0.0295-0.09260.4335-0.13680.46050.1424-0.54990.01720.3799-0.07740.17260.2224-0.01930.264612.057522.466648.5085
60.57060.26080.20011.54460.70971.7922-0.1214-0.0308-0.1510.37170.05140.18830.5049-0.06930.06130.2888-0.0220.07170.1186-0.00760.191617.875518.348847.2272
70.52310.22370.10591.58720.43820.9844-0.04410.01960.0291-0.1051-0.01660.1168-0.0263-0.04020.01360.0647-0.00420.00720.0821-0.02480.110618.01465.13971.954
80.6550.02790.17491.57060.32050.5833-0.03470.01140.0223-0.08190.01390.0047-0.0479-0.00280.04510.0785-0.00580.00850.0961-0.01860.10622.955311.88725.6478
90.32480.10350.12343.1348-0.2681.16270.0604-0.0287-0.04140.1365-0.07660.0710.13770.0470.05630.1266-0.00730.00080.135-0.04080.114921.694312.505322.8064
100.3405-0.0060.01720.64420.64130.67-0.0344-0.02060.0683-0.2646-0.11720.3196-0.0446-0.29420.06360.23610.0312-0.09790.2044-0.03510.279910.531723.01462.1619
110.3513-0.3961-0.27871.68611.00262.1768-0.0602-0.01930.124-0.3406-0.02330.1959-0.4313-0.0210.05260.18160.0125-0.04360.1132-0.02360.198516.377927.93854.1632
121.0699-0.52830.61852.1020.05871.84530.13120.0840.0973-0.5864-0.2336-0.10380.00820.26480.07920.27640.01040.05210.17660.01430.131952.341328.48-22.435
130.644-0.0351-0.08241.0618-0.3421.1838-0.02570.0724-0.0202-0.2528-0.0417-0.09950.1295-0.0270.05880.1316-0.00410.01690.1142-0.0010.108447.950427.0276-12.4829
140.29350.33040.4520.58690.10451.74040.0072-0.0748-0.0510.2684-0.0431-0.1229-0.18150.09490.06750.1983-0.0036-0.03190.13230.02060.128450.820537.242615.9457
150.5533-0.0157-0.17721.1071-0.07551.1067-0.05480.0008-0.01920.04290.0125-0.00180.071-0.00630.05740.07260.00170.01720.09660.01170.103444.009626.57911.9458
160.8329-0.0825-0.43730.9839-0.52441.4151-0.08420.0397-0.1135-0.0614-0.0461-0.1370.27320.13490.06960.12080.01360.03660.11290.01060.153851.834216.9896-1.2865
170.5775-0.4887-0.01592.59810.11321.3215-0.0607-0.0645-0.05060.1288-0.0116-0.00490.07460.06780.08240.15440.0090.00990.16930.05040.126448.282423.449717.5121
180.7375-0.1006-0.18260.9073-0.23751.0585-0.0414-0.052-0.1223-0.0985-0.1086-0.27930.32330.46860.07770.18530.07650.07550.22440.03210.256760.58313.3493-2.7642
190.77230.3219-0.15310.9058-0.29371.17580.0433-0.1370.01680.3623-0.1383-0.105-0.12090.04170.06350.2196-0.033-0.03670.13130.01520.119251.193218.587863.5257
200.4985-0.3258-0.22010.6524-0.03171.6684-0.050.13370.038-0.2676-0.022-0.06460.25730.00190.06270.2445-0.03530.01430.14320.03290.124450.26438.675832.5505
210.87590.29420.1041.0159-0.26610.9705-0.07410.00910.0890.04240.02830.0387-0.0913-0.02060.05950.1117-0.0089-0.02390.09930.02650.105745.823122.167148.4474
220.4328-0.3490.46051.6775-1.32631.9570.01130.0711-0.00540.0949-0.1242-0.1019-0.06960.30760.1050.1381-0.0513-0.0470.14510.03850.161157.356828.330846.2478
230.51890.10830.14931.83840.2561.3004-0.0340.0595-0.022-0.0395-0.0284-0.0161-0.0145-0.05410.06390.1579-0.0448-0.0180.18730.06080.114947.503621.044330.8856
240.4730.14140.16480.621-0.22870.5108-0.04010.02940.04790.2287-0.1162-0.3771-0.05440.46840.08070.2521-0.0742-0.13380.24450.07510.264864.139429.628151.2665
250.60360.4667-0.29891.0971-0.96282.0991-0.0144-0.03590.11950.2492-0.1527-0.2121-0.51880.3420.03650.2405-0.0894-0.08920.17120.04930.208259.88336.109249.4434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 210 )
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 241 )
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 266 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 210 )
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 241 )
11X-RAY DIFFRACTION11chain 'B' and (resid 242 through 266 )
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 20 )
13X-RAY DIFFRACTION13chain 'C' and (resid 21 through 64 )
14X-RAY DIFFRACTION14chain 'C' and (resid 65 through 100 )
15X-RAY DIFFRACTION15chain 'C' and (resid 101 through 150 )
16X-RAY DIFFRACTION16chain 'C' and (resid 151 through 181 )
17X-RAY DIFFRACTION17chain 'C' and (resid 182 through 210 )
18X-RAY DIFFRACTION18chain 'C' and (resid 211 through 265 )
19X-RAY DIFFRACTION19chain 'D' and (resid 6 through 64 )
20X-RAY DIFFRACTION20chain 'D' and (resid 65 through 100 )
21X-RAY DIFFRACTION21chain 'D' and (resid 101 through 165 )
22X-RAY DIFFRACTION22chain 'D' and (resid 166 through 181 )
23X-RAY DIFFRACTION23chain 'D' and (resid 182 through 210 )
24X-RAY DIFFRACTION24chain 'D' and (resid 211 through 241 )
25X-RAY DIFFRACTION25chain 'D' and (resid 242 through 266 )

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