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- PDB-7lao: Crystal structure of aminoglycoside acetyltransferase AAC(3)-IIb -

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Basic information

Entry
Database: PDB / ID: 7lao
TitleCrystal structure of aminoglycoside acetyltransferase AAC(3)-IIb
ComponentsAminoglycoside N(3)-acetyltransferase III
KeywordsTRANSFERASE / AAC(3)-IIb / RESISTANCE / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID
Function / homologyaminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / Aminoglycoside N(3)-acetyltransferase III
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsStogios, P.J. / Evdokimova, E. / Osipiuk, J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: Aminoglycoside N(3)-acetyltransferase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2803
Polymers29,0181
Non-polymers2632
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.174, 61.434, 112.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Aminoglycoside N(3)-acetyltransferase III / ACC(3)-III / Aminocyclitol 3-N-acetyltransferase type III / Gentamicin-(3)-N-acetyl-transferase


Mass: 29017.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: aac3-Vb / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Gold
References: UniProt: Q01515, aminoglycoside 3-N-acetyltransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M citric acid, Bis-tris propane pH 6.4, 25% (w/v) PEG3350, 2 mM magnesium chloride, 1 mM tobramycin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 22563 / % possible obs: 95.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.037 / Net I/σ(I): 26.2
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 935 / CC1/2: 0.983 / Rpim(I) all: 0.159 / % possible all: 79.8

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bc3

6bc3


Resolution: 1.92→35.32 Å / SU ML: 0.2062 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1127 5 %RANDOM
Rwork0.1798 21401 --
obs0.1823 22528 95.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.48 Å2
Refinement stepCycle: LAST / Resolution: 1.92→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 1 203 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01372110
X-RAY DIFFRACTIONf_angle_d1.25972871
X-RAY DIFFRACTIONf_chiral_restr0.0815312
X-RAY DIFFRACTIONf_plane_restr0.0092380
X-RAY DIFFRACTIONf_dihedral_angle_d20.02775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-20.29371140.23582168X-RAY DIFFRACTION79.04
2-2.110.26721360.21312574X-RAY DIFFRACTION93.51
2.11-2.240.24841430.20152724X-RAY DIFFRACTION98.93
2.24-2.410.23181450.18892752X-RAY DIFFRACTION98.87
2.41-2.660.25041440.18342727X-RAY DIFFRACTION98.22
2.66-3.040.24991460.18722772X-RAY DIFFRACTION99.25
3.04-3.830.23071470.17382801X-RAY DIFFRACTION98.76
3.83-35.320.19791520.16272883X-RAY DIFFRACTION96.84
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)
11.88212744482-0.0567436969332-0.5810945238934.2340828814-0.1901722651361.31949495879-0.0304198993418-0.233853189725-0.121309390190.2200662984140.00674565043026-0.8294566453440.03703658606110.2622590170250.01630108734990.1719404309540.020911433072-0.0537320434980.2273474546860.02991987232590.51237691773611.1981267139-5.08674868365-22.6521052016
21.44068191053-0.2804733852-0.532227558020.59420394314-1.286033963173.93383852960.191564356859-1.69456120021.625403697911.864229868440.35084617124-0.329119013047-1.449299957550.634981784166-0.05958690675771.42326794125-0.0364237674243-0.2858158781850.985434859321-0.1968878798610.7061180559358.263817175679.646881025312.55001776015
33.158940076430.697990875978-0.1734333250443.6212580338-0.6373232708761.860974506790.0150138867053-0.3481891340260.3760451143490.6882559867370.0166769266041-0.206382591611-0.2749738905110.00851578730957-0.03481988392110.3233379628990.035637448428-0.04976949949940.19798743757-0.04419377632860.3805567153120.6718682133611.81904025641-15.3240171058
43.558302074571.114708840180.6854692506313.842460543531.36470949820.995195863667-0.656569851651-0.5227150758240.9666281387061.230334166480.7661307552740.0666899701395-1.442860911460.180166232363-0.06075370850651.2624337871-0.100172467946-0.1809274103530.466474954343-0.2467469903160.674386460806-1.0599655096210.184087108-3.77249816917
56.29947058181-0.497472185613-3.372301422764.027847326821.19578741424.60720659581-0.138796199361-0.370480622549-0.4501254424110.451375244828-0.02414280208280.2345366912350.137677709741-0.1529209880410.1759055791060.238572382380.0156048880976-0.004948415056670.1850079307150.0389482684670.44655642439-6.8301529316-13.3789891433-17.351831229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 189 )
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 269 )

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