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- PDB-7q0q: Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B -

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Basic information

Entry
Database: PDB / ID: 7q0q
TitleAcetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B
ComponentsAminoglycoside N(3)-acetyltransferase III
KeywordsANTIBIOTIC / acetyltrasferase / aminoglycosides / inhibitor / complex
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
3N methyl nemycin B / ACETATE ION / DI(HYDROXYETHYL)ETHER / Aminoglycoside N(3)-acetyltransferase III
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsPontillo, N. / Guskov, A.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)694610European Union
H2020 Marie Curie Actions of the European Commission713482European Union
CitationJournal: To Be Published
Title: The 3-N-alkylation of the neomycin B outmaneuvers the aminoglycoside resistant enzyme acetyltransferase(3)IIIa via an unexpected mechanism
Authors: Pontillo, N. / Warszawik, E.M. / Partipilo, M. / Stetsenko, A. / Loznik, M. / Yang, X. / Slotboom, D.J. / Guskov, A. / Herrmann, A.
History
DepositionOct 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,94310
Polymers58,8592
Non-polymers1,0848
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-35 kcal/mol
Surface area23310 Å2
Unit cell
Length a, b, c (Å)64.590, 89.235, 103.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29429.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aacC3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P29808, aminoglycoside 3-N-acetyltransferase

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Non-polymers , 6 types, 501 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-8I5 / 3N methyl nemycin B


Mass: 628.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H48N6O13 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.34 % / Description: orthorombic
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 7-14% PEG 10,000, 0.1 M Na Acetate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.96→19.67 Å / Num. obs: 43209 / % possible obs: 99.13 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1743 / Net I/σ(I): 8.04
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 3999 / CC1/2: 0.551

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Processing

Software
NameVersionClassification
XDS1.19.2_4158data reduction
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ht0,7kes,6mb9,6np4

5ht0

7kes

6mb9

6np4


Resolution: 1.96→19.87 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.2587
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 4026 4.93 %
Rwork0.1896 77685 -
obs0.1918 81711 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.43 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 69 493 4631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824303
X-RAY DIFFRACTIONf_angle_d1.03855880
X-RAY DIFFRACTIONf_chiral_restr0.0586659
X-RAY DIFFRACTIONf_plane_restr0.0078766
X-RAY DIFFRACTIONf_dihedral_angle_d9.1807633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.3471070.33872019X-RAY DIFFRACTION75.52
1.98-2.010.3881610.32962568X-RAY DIFFRACTION95.12
2.01-2.030.32061270.31822671X-RAY DIFFRACTION98.42
2.03-2.060.33581040.31422707X-RAY DIFFRACTION98.94
2.06-2.090.36651290.29992714X-RAY DIFFRACTION99.54
2.09-2.120.32371510.2962700X-RAY DIFFRACTION99.89
2.12-2.150.31841520.28422714X-RAY DIFFRACTION99.93
2.15-2.180.28331600.27492669X-RAY DIFFRACTION100
2.18-2.220.35211360.26482727X-RAY DIFFRACTION100
2.22-2.260.30431400.26662680X-RAY DIFFRACTION99.93
2.26-2.30.28121340.24162792X-RAY DIFFRACTION99.93
2.3-2.340.24791660.23562642X-RAY DIFFRACTION100
2.34-2.390.27041430.23092704X-RAY DIFFRACTION99.96
2.39-2.440.2941580.23372678X-RAY DIFFRACTION99.93
2.44-2.50.24281370.22622724X-RAY DIFFRACTION99.97
2.5-2.560.28691090.22222725X-RAY DIFFRACTION99.82
2.56-2.630.24141600.2132679X-RAY DIFFRACTION99.93
2.63-2.710.29051110.20132774X-RAY DIFFRACTION99.93
2.71-2.790.26481470.19412688X-RAY DIFFRACTION99.89
2.79-2.890.2741330.2112730X-RAY DIFFRACTION100
2.89-3.010.20791280.18352684X-RAY DIFFRACTION99.96
3.01-3.140.27171510.17382713X-RAY DIFFRACTION99.93
3.14-3.310.21871220.18242713X-RAY DIFFRACTION100
3.31-3.520.21241540.14932715X-RAY DIFFRACTION99.97
3.52-3.790.18411300.1452729X-RAY DIFFRACTION99.9
3.79-4.160.20611530.13572668X-RAY DIFFRACTION99.93
4.16-4.760.17841360.12592724X-RAY DIFFRACTION100
4.76-5.970.15791470.14372721X-RAY DIFFRACTION100
5.97-19.870.1861400.15722713X-RAY DIFFRACTION99.93

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