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- PDB-7kes: Crystal structure of meta-AAC0038, an environmental aminoglycosid... -

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Basic information

Entry
Database: PDB / ID: 7kes
TitleCrystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in complex with apramycin and CoA
ComponentsAminoglycoside N(3)-acetyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / ANTIBIOTIC_NAT FAMILY / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / CSGID / TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID / 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 / APRAMYCIN / COENZYME A / Aminoglycoside N(3)-acetyltransferase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsStogios, P.J. / Skarina, T. / Michalska, K. / Xu, Z. / Yim, V. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / 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
DepositionOct 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,32711
Polymers57,3092
Non-polymers3,0189
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-13 kcal/mol
Surface area23000 Å2
Unit cell
Length a, b, c (Å)127.766, 127.766, 94.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aminoglycoside N(3)-acetyltransferase


Mass: 28654.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: PMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -MAGIC
References: UniProt: A0A059X981, aminoglycoside 3-N-acetyltransferase

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Non-polymers , 5 types, 176 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE


Mass: 539.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41N5O11 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 50mM ADA pH 7, 10 mM apramycin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 36915 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 56.89 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Net I/σ(I): 21.9
Reflection shellResolution: 2.36→2.4 Å / Rmerge(I) obs: 1.427 / Mean I/σ(I) obs: 1 / Num. unique obs: 1816 / CC1/2: 0.601 / Rpim(I) all: 0.505 / % possible all: 100

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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: 5HT0

5ht0


Resolution: 2.36→29.19 Å / SU ML: 0.3252 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1846 5.01 %RANDOM
Rwork0.1905 35033 --
obs0.1924 36879 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.64 Å2
Refinement stepCycle: LAST / Resolution: 2.36→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 195 167 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474288
X-RAY DIFFRACTIONf_angle_d1.33695846
X-RAY DIFFRACTIONf_chiral_restr0.0684652
X-RAY DIFFRACTIONf_plane_restr0.0057740
X-RAY DIFFRACTIONf_dihedral_angle_d19.71991606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.430.34671370.2962628X-RAY DIFFRACTION99.25
2.43-2.50.3041390.26962641X-RAY DIFFRACTION99.93
2.5-2.580.29721440.25782681X-RAY DIFFRACTION99.93
2.58-2.670.29431380.24342675X-RAY DIFFRACTION99.96
2.67-2.780.25971440.22912682X-RAY DIFFRACTION100
2.78-2.90.24571430.2342687X-RAY DIFFRACTION100
2.9-3.050.2921440.23832693X-RAY DIFFRACTION100
3.05-3.250.28491450.22122666X-RAY DIFFRACTION99.96
3.25-3.50.23931410.20412678X-RAY DIFFRACTION100
3.5-3.850.23071400.18722704X-RAY DIFFRACTION100
3.85-4.40.20611410.15932733X-RAY DIFFRACTION100
4.4-5.540.18721420.15652742X-RAY DIFFRACTION100
5.54-29.190.19161480.16832823X-RAY DIFFRACTION99.76
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)
13.88317501191-3.92724241858-1.05706513074.63910009815-0.7361852062387.266573473670.0707525754243-0.195583151457-0.0193323868014-0.0289662224193-0.0791106774173-0.140227210387-0.3700001891090.7478643403820.04735435404140.263289543382-0.153830789769-0.0333653791120.466759070554-0.001445011363350.42913815456821.5357284282-53.8307250941-1.82544750811
29.00842274279-0.0476976218078-4.822586199938.407322750175.089952314658.216352031810.104491672736-0.497456343091.535287571410.1245949022470.0424543061388-0.331820145804-0.800851684132-0.611707006234-0.1546132266010.425761666586-0.1454496812690.02259304987110.3972287522490.06814591153680.4207879449323.14403589786-52.9831484312.38761382771
37.15031582337-0.6971904059991.619360621424.96641576999-3.290643813033.03918413228-0.0587616672288-0.2971158548920.3759531656280.3277560620060.4166055118960.982001912125-0.9595713916-1.44538819488-0.2747979566460.5488230966640.2070233592910.0214143893150.9979599805740.1602065539620.652446702169-10.9476768696-47.6691342633-1.62555484945
44.346885772740.9493289952160.4759038439281.209770935290.5017008955523.588365506170.0869341855574-0.5549054960260.1800659397850.1910068974760.02678696276450.0689332018724-0.378674057733-0.296161749022-0.1000070255530.384964334792-0.0389212894670.01293497552170.5602421435190.05744778119430.445043869525.19887347939-51.658132697912.4035266463
56.810552659153.007129196122.41051250622.179120435141.420513706728.42225802998-0.06257154253710.3693470085990.35815524462-0.1709285137760.1350115874620.555421368734-0.503435827598-1.37314611225-0.006466973325410.3963280110980.0465385645747-0.05407572240610.9926865551320.2875408264150.677565349909-11.1838527374-45.3591696058-18.2280676211
64.66251857607-2.30769409894-1.620209898412.94322983147-1.037900111533.728222168530.08949317684520.265291843850.248414810241-0.02723376343960.12897407421-0.252429680407-0.131485657516-0.0903791522063-0.1978407966310.425684993664-0.1501715637970.007653410851430.500948689879-0.05471310617680.3591681387915.1893984882-53.309561498-20.1148755218
72.83110026096-0.93976896451-1.194360411651.976728034230.04615880962392.77459569852-0.08592203653151.101746984150.0395349772963-0.5040213335140.1408447373910.15433079633-0.0342687747477-0.670782043226-0.05672819127660.508251471145-0.209706909821-0.03593387751890.8679986631780.0487708373780.4771095358567.48450388066-53.6807532109-29.3324169926
82.62528443139-1.591961049520.08250403997953.65963051932-0.7505207831662.803714867940.1234470095871.341870513440.762009750278-0.8425260104150.04874141326750.221801843899-0.360334357634-0.976739130967-0.1960633614450.895323006018-0.00343648210243-0.1614578333311.342932528370.3681304177540.741403188083-0.186095379096-39.902195144-38.4287415716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 262 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 262 )

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