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- PDB-7q10: Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B -

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Basic information

Entry
Database: PDB / ID: 7q10
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 / antibiotic metabolic process / aminoglycoside 3-N-acetyltransferase / 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: 1.82 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: 3-N-alkylation in aminoglycoside antibiotic neomycin B overcomes bacterial resistance mediated by acetyltransferase (3) IIIa
Authors: Pontillo, N. / Warszawik, E.M. / Partipilo, M. / Stetsenko, A. / Loznik, M. / Yang, X. / Slotboom, D.J. / Guskov, A. / Herrmann, A.
History
DepositionOct 17, 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)60,47415
Polymers58,8592
Non-polymers1,61613
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-19 kcal/mol
Surface area23180 Å2
Unit cell
Length a, b, c (Å)89.004, 103.122, 64.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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, 506 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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: 2.52 Å3/Da / Density % sol: 51.13 %
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: P14 (MX2) / 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: 1.82→54.72 Å / Num. obs: 53217 / % possible obs: 98.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 26.87 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.72
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 4801 / CC1/2: 0.287

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q0Q

7q0q


Resolution: 1.82→54.72 Å / SU ML: 0.2524 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 2619 4.94 %
Rwork0.1948 50411 -
obs0.1966 53030 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.75 Å2
Refinement stepCycle: LAST / Resolution: 1.82→54.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 105 493 4665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794312
X-RAY DIFFRACTIONf_angle_d1.01225875
X-RAY DIFFRACTIONf_chiral_restr0.0595657
X-RAY DIFFRACTIONf_plane_restr0.0071758
X-RAY DIFFRACTIONf_dihedral_angle_d10.2915639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.850.38571120.33152298X-RAY DIFFRACTION86.07
1.85-1.890.35291170.332468X-RAY DIFFRACTION91.99
1.89-1.930.34531230.30612645X-RAY DIFFRACTION99.18
1.93-1.970.32931370.27982633X-RAY DIFFRACTION99.25
1.97-2.010.30491330.26952685X-RAY DIFFRACTION99.4
2.02-2.070.30691310.26272670X-RAY DIFFRACTION99.5
2.07-2.120.29081480.2562623X-RAY DIFFRACTION99.39
2.12-2.180.30941500.23462643X-RAY DIFFRACTION99.4
2.18-2.250.24491580.21682639X-RAY DIFFRACTION99.33
2.25-2.330.25721370.20242682X-RAY DIFFRACTION99.37
2.33-2.430.22261440.20232652X-RAY DIFFRACTION99.18
2.43-2.540.22631220.19872696X-RAY DIFFRACTION99.44
2.54-2.670.26541570.19922660X-RAY DIFFRACTION99.44
2.67-2.840.28861510.20232660X-RAY DIFFRACTION99.15
2.84-3.060.23091480.19052677X-RAY DIFFRACTION98.78
3.06-3.370.20951310.17412708X-RAY DIFFRACTION99.27
3.37-3.850.19011460.15632730X-RAY DIFFRACTION99.55
3.85-4.860.15931540.14232740X-RAY DIFFRACTION99.01
4.86-54.720.21711200.18152902X-RAY DIFFRACTION98.95
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)
10.4157070653520.0180687255423-0.3155456601710.351425021704-0.08940466730940.179975493657-0.198940673335-0.564695432883-0.3210374306570.3544816954690.1715197113990.06448675642090.419260111003-0.2617142812450.004531308568180.3597296792140.0707039594994-0.02041038296710.295909020590.0117308459130.21253946672614.43822466848.874756483820.2804742171
20.529326384106-0.1877622308470.1566611288190.73025709917-0.1446651572030.5872209072140.03839430955480.0441520224908-0.0397648982725-0.0594286427524-0.0253290342792-0.02927888795820.0694508819160.0278157429852-2.31346385577E-50.206694311120.03224502116130.002718766853420.201073204376-0.01359617813070.1602757781213.952158538818.364800533111.7232345859
30.723472030097-0.02920684295570.5791346038810.1153917098450.1024055347970.541709307258-0.0882446829924-0.0937444221910.09800489638030.03851381866730.0638101035473-0.05636078144190.0144348010601-0.1229176070118.5800991818E-60.216620952880.0171435027809-0.008390431403710.265821265934-0.02221073797140.26280881429323.451205855147.151520027917.7191258627
40.831777101728-0.0552026237939-0.003152247383351.45326159586-0.2746869968950.4741616654870.0143432233622-0.02412874050530.09556168891210.0276195062085-0.0357376476406-0.0346478324957-0.04097917863040.08334966934234.08580845143E-50.1725719199530.0109683631886-0.008304889800250.203394855401-0.005746505284010.15595741082811.182934979431.57401845619.86372377062
50.350209828032-0.2445497605040.2998609498040.6421119796060.008658347160720.29795894992-0.10086495981-0.00852977816945-0.2290622255940.0503306225942-0.0419745863587-0.029189612659-0.03895033690690.04342533582444.81652715071E-60.2465305905170.01007004199-0.01181980894820.2202786045920.02360420336640.26321790124212.677063174548.467927509611.1159565456
60.437812609013-0.4676118216140.2706980148640.6524247339220.2191841655360.204311971562-0.166815387247-0.100341796075-0.07154370104110.4442121956440.115938659540.154774019746-0.0637265811967-0.165281572725-8.23903426818E-50.2852618074730.01772384237020.07877225901380.2596726253490.05163058066190.2930353806750.083952981920731.576379749120.4179337008
70.329812768123-0.04839397266070.1122511600960.4756039490170.0663106178433-0.02610063966980.0685887240365-0.0602344866212-0.1739375956930.01238690408320.08981145599620.6504632144450.0620299740161-0.1073049472290.01687045772920.210607898345-0.001932880934470.06743216634290.213237794436-0.007576659461010.406979184812-5.9326035972930.769923399815.4917875435
81.391797627040.3319510003670.090834199880.158681716502-0.05167843253860.109646416158-0.27119219340.705884500761-1.10669029476-0.1082637848140.227461442171-0.03966141113640.3579426123730.08751962630340.001005706377580.2362981412950.00127547807060.004045228223690.184916284277-0.06179604386890.339933233674-4.663973343745.0142305988742.9150764985
90.465330306297-0.116883562329-0.06528734603930.854943198017-0.0869876920246-0.0596417805048-0.0547034971163-0.0514823526931-0.03496747803290.02545344462720.1170697129740.0564565244971-0.00824114020619-0.0186840555296-3.9475214043E-60.198036451252-0.00345091870987-0.004157144249640.2026545831140.003027465611150.171332219923-8.6932027500327.85703962847.1035764687
100.263223440444-0.3441022973110.0002918381484490.3336373899770.033729160320.01639122704040.07322170746030.0541330141817-0.105827585546-0.152422500535-0.04882832888160.0799241225544-0.11274120464-0.05017588963240.0001378575614570.24542253306-0.020491180671-0.009750140473170.214342313785-0.01136108584090.25351817927-8.9765429491526.471779503349.5291723809
110.6385457935340.054089633033-0.3528858677770.4165641417220.4886818579770.4347509360270.0195605322282-0.0604129371795-0.01586057833980.03011714617850.0487209327708-0.0514456782151-0.02110661085370.05249022123362.9662787328E-50.178929094809-0.00435886650368-0.01241084014830.186973680963-0.003706693679940.1620085026784.3906083384228.040609308948.8462417269
120.258861552047-0.003967010399460.2948195608540.3063107684170.1378791808720.471609704367-0.0127287259645-0.08344650886110.14971378239-0.04978343287550.0663776586927-0.0350839330305-0.04767017652260.03512429543630.0001123968860620.24667942841-0.01910748334280.008646410173010.2099550236230.002077490982080.20601682057-0.33906822310644.610688673848.7444995927
130.352979401360.3099845368720.01758419750220.292127880691-0.03783477022970.336264855688-0.03143839500190.139350211737-0.117485230614-0.282770786915-0.0384193169750.1272626183510.00189399256306-0.0538166424234-5.19907894231E-50.2693298486180.0008920853511860.02783023485610.262987079907-0.04826550469340.2253674113397.3831537089925.135112992333.8322539473
140.594180994676-0.350533960232-0.05675355954220.220605413504-0.04337273209010.0483415366166-0.04257665339630.107280683886-0.0927525856405-0.07044856883510.0738163490423-0.307564237066-0.00697032840549-0.006344554124098.19801595067E-50.20761272722-0.00793855841530.0235762636760.248622262947-0.04269563005850.21784467132213.744187096726.216952334638.6702739216
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 40 )AA21 - 401 - 20
22chain 'A' and (resid 41 through 84 )AA41 - 8421 - 64
33chain 'A' and (resid 85 through 118 )AA85 - 11865 - 98
44chain 'A' and (resid 119 through 201 )AA119 - 20199 - 181
55chain 'A' and (resid 202 through 226 )AA202 - 226182 - 205
66chain 'A' and (resid 227 through 261 )AA227 - 261206 - 240
77chain 'A' and (resid 262 through 288 )AA262 - 288241 - 267
88chain 'B' and (resid 26 through 40 )BH26 - 401 - 15
99chain 'B' and (resid 41 through 118 )BH41 - 11816 - 93
1010chain 'B' and (resid 119 through 145 )BH119 - 14594 - 120
1111chain 'B' and (resid 146 through 201 )BH146 - 201121 - 176
1212chain 'B' and (resid 202 through 230 )BH202 - 230177 - 205
1313chain 'B' and (resid 231 through 261 )BH231 - 261206 - 236
1414chain 'B' and (resid 262 through 286 )BH262 - 286237 - 261

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