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- PDB-6mb5: AAC-IIIb binary with NEOMYCIN -

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Basic information

Entry
Database: PDB / ID: 6mb5
TitleAAC-IIIb binary with NEOMYCIN
ComponentsAac(3)-IIIb protein
KeywordsTRANSFERASE/ANTIBIOTIC / acetyltransferase / promiscuity / GNAT / antibiotic resistance / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC complex
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / NEOMYCIN / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsCuneo, M.J. / Kumar, P.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Encoding of Promiscuity in an Aminoglycoside Acetyltransferase.
Authors: Kumar, P. / Selvaraj, B. / Serpersu, E.H. / Cuneo, M.J.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6332
Polymers29,0191
Non-polymers6151
Water2,378132
1
A: Aac(3)-IIIb protein
hetero molecules

A: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2674
Polymers58,0382
Non-polymers1,2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3940 Å2
ΔGint4 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.120, 106.120, 68.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Aac(3)-IIIb protein


Mass: 29018.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aac(3)-IIIb / Production host: Escherichia coli DH1 (bacteria) / Strain (production host): DH1 / References: UniProt: Q51405
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N6O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Sequence detailssee NCBI Reference Sequence: WP_088170001.1

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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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1-3%PEG 4000, 20-25% isopropanol,0.1M HEPES, pH=7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.951 Å / Num. obs: 22720 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.15 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.055 / Rrim(I) all: 0.107 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.273.30.53419330.880.3340.63497.8
9.07-45.953.50.0483680.9950.0290.05798.9

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 2.2→45.951 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62
RfactorNum. reflection% reflection
Rfree0.2608 1138 5.03 %
Rwork0.2446 --
obs0.2454 22640 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.02 Å2 / Biso mean: 44.6403 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 2.2→45.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 0 132 2164
Biso mean---43.03 -
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30020.36551130.36552666277996
2.3002-2.42140.33651540.32362606276098
2.4214-2.57310.32981360.32142638277498
2.5731-2.77180.33811290.31192664279398
2.7718-3.05070.33631310.29622675280698
3.0507-3.4920.27271590.26192687284699
3.492-4.3990.23021520.212727562908100
4.399-45.96130.20261640.17842810297499

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