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- PDB-6mb7: Binary (paromomycin) structure of AAC-IIIb -

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Basic information

Entry
Database: PDB / ID: 6mb7
TitleBinary (paromomycin) structure of AAC-IIIb
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 / PAROMOMYCIN / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)29,6342
Polymers29,0191
Non-polymers6161
Water3,315184
1
A: Aac(3)-IIIb protein
hetero molecules

A: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2694
Polymers58,0382
Non-polymers1,2312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4020 Å2
ΔGint-20 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.190, 106.190, 69.000
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-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1-3% PEG 4000, 20-25% isopropanol and 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 S 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→38.26 Å / Num. obs: 22425 / % possible obs: 97.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 34.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.051 / Rrim(I) all: 0.087 / Net I/σ(I): 9.8 / Num. measured all: 59188 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.272.60.513503619660.7720.3880.646298.1
9.07-38.262.50.0229063590.9980.0160.02734.897.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BC3

6bc3


Resolution: 2.2→38.264 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1187 5.3 %
Rwork0.2002 21193 -
obs0.2022 22380 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.51 Å2 / Biso mean: 42.0477 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 2.2→38.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 42 184 2216
Biso mean--48.64 45.46 -
Num. residues----265
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 (%)
2.2001-2.30020.32321070.30312723283098
2.3002-2.42150.29231690.27032582275197
2.4215-2.57320.29881410.25172561270295
2.5732-2.77180.28381680.23412611277997
2.7718-3.05060.29451430.23232647279097
3.0506-3.49180.25571490.20472609275895
3.4918-4.39820.19621440.16822697284197
4.3982-38.26950.18451660.15822763292997

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