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- PDB-4qc6: Crystal structure of aminoglycoside 6'-acetyltransferase-Ie -

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Basic information

Entry
Database: PDB / ID: 4qc6
TitleCrystal structure of aminoglycoside 6'-acetyltransferase-Ie
ComponentsBifunctional AAC/APH
Keywordstransferase/antibiotic / antibiotic resistance / GNAT family / acetyltransferase / acetylcoenzyme-A / aminoglycoside / transferase / transferase-antibiotic complex
Function / homology
Function and homology information


aminoglycoside 2''-phosphotransferase / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / kinase activity / response to antibiotic / ATP binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) domain / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Protein kinase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-30N / FORMIC ACID / KANAMYCIN A / Bifunctional AAC/APH
Similarity search - Component
Biological speciesStaphylococcus warneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSmith, C.A. / Toth, M. / Weiss, T.M. / Frase, H. / Vakulenko, S.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the bifunctional aminoglycoside-resistance enzyme AAC(6')-Ie-APH(2'')-Ia revealed by crystallographic and small-angle X-ray scattering analysis.
Authors: Smith, C.A. / Toth, M. / Weiss, T.M. / Frase, H. / Vakulenko, S.B.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional AAC/APH
B: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,27011
Polymers43,4712
Non-polymers2,7989
Water12,701705
1
A: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1125
Polymers21,7361
Non-polymers1,3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional AAC/APH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1586
Polymers21,7361
Non-polymers1,4225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.830, 89.720, 96.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional AAC/APH / 6'-aminoglycoside N-acetyltransferase / AAC(6') / 2''-aminoglycoside phosphotransferase / APH(2'')


Mass: 21735.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus warneri (bacteria) / Gene: aacA-aphD / Production host: Escherichia coli (E. coli)
References: UniProt: Q7ATH7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-KAN / KANAMYCIN A / Kanamycin A


Mass: 484.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-30N / (3R,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3,5-diphosphaheptadecane-17-sulfinic acid 3,5-dioxide (non-preferred name)


Mass: 799.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O18P3S
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: unbuffered 0.2 M ammonium formate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→19.941 Å / Num. all: 112448 / Num. obs: 112448 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.1
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.4 / % possible all: 87.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→19.941 Å / SU ML: 0.09 / σ(F): 1.37 / Phase error: 14.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1661 5671 5.04 %random 5%
Rwork0.1466 ---
all0.1476 112422 --
obs0.1476 112422 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 181 705 3954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063541
X-RAY DIFFRACTIONf_angle_d1.2924838
X-RAY DIFFRACTIONf_dihedral_angle_d19.9881445
X-RAY DIFFRACTIONf_chiral_restr0.056516
X-RAY DIFFRACTIONf_plane_restr0.006594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.25791520.2092927X-RAY DIFFRACTION82
1.3148-1.33020.2421630.19463380X-RAY DIFFRACTION94
1.3302-1.34650.20621640.18253482X-RAY DIFFRACTION97
1.3465-1.36350.21642030.16783449X-RAY DIFFRACTION98
1.3635-1.38140.18341840.1573539X-RAY DIFFRACTION99
1.3814-1.40040.18431860.15033561X-RAY DIFFRACTION99
1.4004-1.42040.18962010.14223535X-RAY DIFFRACTION100
1.4204-1.44150.161840.13483532X-RAY DIFFRACTION100
1.4415-1.46410.16322000.13573598X-RAY DIFFRACTION100
1.4641-1.48810.16551800.12843556X-RAY DIFFRACTION100
1.4881-1.51370.16031900.12243598X-RAY DIFFRACTION100
1.5137-1.54120.16251740.11573554X-RAY DIFFRACTION100
1.5412-1.57090.14172030.11683572X-RAY DIFFRACTION100
1.5709-1.60290.16171990.12123572X-RAY DIFFRACTION100
1.6029-1.63780.17782020.12143533X-RAY DIFFRACTION100
1.6378-1.67580.15161820.12143614X-RAY DIFFRACTION100
1.6758-1.71770.16341840.12323573X-RAY DIFFRACTION100
1.7177-1.76410.16841920.13193616X-RAY DIFFRACTION100
1.7641-1.8160.171980.13693553X-RAY DIFFRACTION100
1.816-1.87460.16691980.14243580X-RAY DIFFRACTION100
1.8746-1.94150.15762090.14363579X-RAY DIFFRACTION100
1.9415-2.01920.16361840.1383601X-RAY DIFFRACTION100
2.0192-2.1110.15491810.13873620X-RAY DIFFRACTION100
2.111-2.22220.14852050.14213592X-RAY DIFFRACTION100
2.2222-2.36120.1731830.14993602X-RAY DIFFRACTION100
2.3612-2.54310.1891860.16293639X-RAY DIFFRACTION100
2.5431-2.79850.1661960.16453631X-RAY DIFFRACTION100
2.7985-3.2020.16761970.16023642X-RAY DIFFRACTION100
3.202-4.02870.17351970.14833691X-RAY DIFFRACTION99
4.0287-19.94370.14231940.14953830X-RAY DIFFRACTION99

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