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- PDB-6mb9: Ternary (neomycin/CoA) structure of AAC-IIIb -

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Basic information

Entry
Database: PDB / ID: 6mb9
TitleTernary (neomycin/CoA) 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 / COENZYME A / NEOMYCIN / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Aac(3)-IIIb protein
C: Aac(3)-IIIb protein
D: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,01813
Polymers116,0754
Non-polymers5,9439
Water4,486249
1
A: Aac(3)-IIIb protein
C: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2167
Polymers58,0382
Non-polymers3,1795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint3 kcal/mol
Surface area21680 Å2
MethodPISA
2
B: Aac(3)-IIIb protein
D: Aac(3)-IIIb protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8026
Polymers58,0382
Non-polymers2,7644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint4 kcal/mol
Surface area21400 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
ΔGint-5 kcal/mol
Surface area39770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.043, 69.168, 69.837
Angle α, β, γ (deg.)88.800, 64.360, 80.530
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 271)
21(chain B and resid 1 through 271)
31(chain C and resid 1 through 271)
41(chain D and resid 1 through 271)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 1 through 271)A1 - 271
211(chain B and resid 1 through 271)B1 - 271
311(chain C and resid 1 through 271)C1 - 271
411(chain D and resid 1 through 271)D1 - 271

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Components

#1: Protein
Aac(3)-IIIb protein


Mass: 29018.799 Da / Num. of mol.: 4
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-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-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical
ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H46N6O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14-22% PEG 3350 and 0.1-0.4M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 37666 / % possible obs: 97.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.98 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.073 / Rrim(I) all: 0.108 / Χ2: 0.573 / Net I/σ(I): 4.9 / Num. measured all: 72266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.591.80.32337100.7980.2980.440.46196.5
2.59-2.691.90.27137050.8240.2490.3690.48395.9
2.69-2.821.90.22737440.8870.210.310.49997.1
2.82-2.9620.19237230.9210.1770.2610.50996.7
2.96-3.1520.13237980.9590.1220.1810.53797.6
3.15-3.391.90.09637290.9770.0880.130.64397.7
3.39-3.731.90.06838150.9870.0620.0930.65798.7
3.73-4.2720.05438210.9910.0490.0730.67998.7
4.27-5.381.90.04237950.9940.0390.0580.63698.8
5.38-5020.03838260.9960.0330.050.6199

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BC3

6bc3


Resolution: 2.5→48.8 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.72
RfactorNum. reflection% reflection
Rfree0.2265 1874 5 %
Rwork0.1987 --
obs0.2001 37663 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.21 Å2 / Biso mean: 30.9665 Å2 / Biso min: 14.02 Å2
Refinement stepCycle: final / Resolution: 2.5→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8135 0 364 249 8748
Biso mean--33.55 29.12 -
Num. residues----1065
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4932X-RAY DIFFRACTION11.215TORSIONAL
12B4932X-RAY DIFFRACTION11.215TORSIONAL
13C4932X-RAY DIFFRACTION11.215TORSIONAL
14D4932X-RAY DIFFRACTION11.215TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4798-2.54680.29711290.24942447257686
2.5468-2.62180.28591370.23992697283496
2.6218-2.70640.31131420.2522751289397
2.7064-2.80310.26371480.24432772292097
2.8031-2.91530.26251540.24292758291297
2.9153-3.0480.27351300.24582769289998
3.048-3.20860.27181540.23192772292698
3.2086-3.40960.27091430.21342767291098
3.4096-3.67280.21311520.18892822297499
3.6728-4.04230.19381500.16962781293199
4.0423-4.62680.18211410.152830297198
4.6268-5.82770.17381540.16982818297299
5.8277-48.80910.19031500.1762795294599

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