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- PDB-7uuo: Crystal structure of aminoglycoside resistance enzyme ApmA H135A ... -

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Basic information

Entry
Database: PDB / ID: 7uuo
TitleCrystal structure of aminoglycoside resistance enzyme ApmA H135A mutant, complex with tobramycin and coenzyme A
ComponentsAminocyclitol acetyltransferase ApmA
KeywordsTRANSFERASE / XAT / XENOBIOTIC ACETYLTRANSFERASE / LEFT-HANDED BETA HELIX / LBH / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDE / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Function / homology: / Trimeric LpxA-like superfamily / transferase activity / metal ion binding / COENZYME A / TOBRAMYCIN / Aminocyclitol acetyltransferase ApmA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsStogios, P.J. / Evdokimova, E. / Michalska, K. / Di Leo, R. / Bordeleau, E. / Wright, G.D. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance.
Authors: Bordeleau, E. / Stogios, P.J. / Evdokimova, E. / Koteva, K. / Savchenko, A. / Wright, G.D.
History
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Structure summary / Category: audit_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminocyclitol acetyltransferase ApmA
B: Aminocyclitol acetyltransferase ApmA
C: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0048
Polymers93,7723
Non-polymers2,2325
Water43224
1
A: Aminocyclitol acetyltransferase ApmA
hetero molecules

A: Aminocyclitol acetyltransferase ApmA
hetero molecules

A: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3619
Polymers93,7723
Non-polymers1,5896
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12440 Å2
ΔGint-48 kcal/mol
Surface area34780 Å2
MethodPISA
2
B: Aminocyclitol acetyltransferase ApmA
hetero molecules

B: Aminocyclitol acetyltransferase ApmA
hetero molecules

B: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4779
Polymers93,7723
Non-polymers3,7056
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16560 Å2
ΔGint-43 kcal/mol
Surface area33200 Å2
MethodPISA
3
C: Aminocyclitol acetyltransferase ApmA
hetero molecules

C: Aminocyclitol acetyltransferase ApmA
hetero molecules

C: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1746
Polymers93,7723
Non-polymers1,4033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area11940 Å2
ΔGint-43 kcal/mol
Surface area34620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.292, 108.292, 87.726
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein Aminocyclitol acetyltransferase ApmA


Mass: 31257.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: apmA / Plasmid: PET19BTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: A0A1D0AST6
#2: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H37N5O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 10% PEG 10K, 2 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: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 33452 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 63.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.052 / Net I/σ(I): 16.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.61 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1674 / CC1/2: 0.638 / Rpim(I) all: 0.605 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JM2

7jm2


Resolution: 2.65→29.45 Å / SU ML: 0.5202 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 40.9392
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3282 1614 4.9 %RANDOM
Rwork0.2856 31327 --
obs0.2877 32941 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.29 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 148 24 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00656850
X-RAY DIFFRACTIONf_angle_d1.08169303
X-RAY DIFFRACTIONf_chiral_restr0.06351026
X-RAY DIFFRACTIONf_plane_restr0.00591190
X-RAY DIFFRACTIONf_dihedral_angle_d18.58872539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.41231220.37042465X-RAY DIFFRACTION93.56
2.72-2.810.38691320.36052570X-RAY DIFFRACTION95.82
2.81-2.910.31731310.35542592X-RAY DIFFRACTION96.66
2.91-3.020.40691330.34012635X-RAY DIFFRACTION97.64
3.02-3.160.43761270.37082634X-RAY DIFFRACTION97.7
3.16-3.330.39461410.34512634X-RAY DIFFRACTION98.93
3.33-3.530.37361500.332639X-RAY DIFFRACTION99.15
3.54-3.810.39311370.29122639X-RAY DIFFRACTION99.14
3.81-4.190.32231330.27382630X-RAY DIFFRACTION98.08
4.19-4.790.29041460.25112654X-RAY DIFFRACTION99.5
4.8-6.030.29041380.25712635X-RAY DIFFRACTION98.23
6.03-29.450.27351240.23682600X-RAY DIFFRACTION96.77
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)
17.50316175688-1.933276495710.1594239892271.39748253421-1.112716040834.274526336120.158387124531-0.1078636825310.08038854003530.137838922851-0.0100134034352-1.5378107802-0.1473647782080.401522668793-0.08286348324370.1814164857030.03818643562650.04511177436920.323165988484-0.07779713830821.0801016470315.9219517852-5.9274766459151.3294656746
24.06994992983-1.095700297680.6208080207381.19235104201-0.3463846201970.01894141675820.06182389249130.88806826305-0.957071611406-0.755653978726-0.13776743108-0.3719654402410.09568735032150.004854606401710.05145006444750.512221234116-0.02008039902430.1278165006040.670430999287-0.2441675106490.83949434831.99569160429-16.839276458230.6445165906
33.11496397025-0.447532258009-1.07744648091.61285262436-0.2070438352422.50543082210.1724849539281.9497952922-0.682771048886-1.23956687369-0.243438380951-0.1754428143260.7398219797660.1843282920990.1696658718410.7390833738680.2353838479730.6909413327231.74029885928-0.2468720514630.57773028066117.5412010059-12.780759821418.2748922616
44.06224653045-2.130311746680.651432051653.432845415610.308928182513.58098172999-0.1076725529650.109779782191.30620237896-0.1231202321930.2288022118330.440569336107-0.298798961661-0.0743143592473-0.06645170627740.2743752840360.0493520778510.09874724880740.293040058356-0.01649959819411.0834076257841.0761859983-20.478767322645.5133180799
52.65456552308-1.676158877750.5758946783742.27345559594-0.1321671628580.0224025993453-0.52215578942-1.029156214630.1449602613961.421375123370.2705522815670.3925177865070.0951912570065-0.4673174841840.1892451249191.007704049980.1943759905790.3657369388210.828416593342-0.1382069729470.77617292823936.2773949899-29.514377603773.0040855758
65.417734215530.8973901849585.290965718246.201155453661.073949514639.17458061484-0.300467234771.46980169154-0.875296986283-0.8294841199890.0846954166775-1.83547112266-0.1890442645391.883161963960.2640985855711.18496117245-0.097049129720.4754215491821.613375708460.03297323841931.8532771840317.6883142948-60.083193241155.2296425475
78.126571578766.04958577982.279994359554.97733701725-0.1355934550777.72276724110.6402478368110.5390006658770.6680694276760.519860734326-0.3987200917490.04528807135761.91986630654-0.24003509876-0.2912565232731.357417630130.4433818592650.04216482551662.57058641295-0.5519885201491.4545401616618.20036082-66.410398787646.997918773
87.481860196780.9641103136725.220173474082.478945110063.133474501766.218470727380.9801924650040.279733930759-1.937717785252.55313352357-2.413709369311.814681811342.88909509026-2.85756245021.302977704931.85280528764-0.5317913399480.4740031027891.84113577357-0.2742584661872.3541388196512.2834830316-72.341232459156.1611504677
91.028524940392.058009518932.28108319064.109621704254.561369960235.057275685170.287726712219-0.219589307552-1.25608518406-1.312369446570.492413859315-1.71034878725-0.09973826144583.25801015316-0.5644836564441.174820687520.4555187870440.2193729755351.51536888262-0.09765686584292.047185643217.9035208144-68.797937703660.1951239775
101.73136451215-1.74196074507-2.210977801887.242978983172.435981508012.73156827576-0.3804822891490.04944649720070.2298604552590.177321083930.07738639262970.142253385422-0.485043153390.7930962606790.2713916518081.099684804920.116880151575-0.2033225284171.503696025040.1512831630491.3882339919310.7804190437-48.080525260176.1555527106
112.466851227181.27270298326-0.4775957974811.477278777852.062654293666.76187898857-1.42483836593-1.340133657761.264578602210.6612140164160.397939435274-0.1518669276950.5940146257030.7003914393110.9250734061691.578350181970.530877361404-0.3183924313521.613599543020.1361517899291.9985562045313.4914396083-50.795705654783.4748990952
124.175982423432.70972914293.555895318725.789303145513.550088003343.409029134750.819048300175-0.05130103116240.8664373500310.832029059439-1.885137189540.7238356042040.0213312256695-1.129702534430.642901078741.878628869470.5789390321070.1051650757471.941255247710.2803884316641.0428862406414.1063466748-56.37854512486.6641082884
139.21871296001-3.76696884558-1.103465868792.852075818450.3592839197347.69768934741-0.652842689642-0.246462360381-1.468246401420.429327846394-0.452936872852-0.01713247947070.100193630462-1.186408346291.124699284180.9506955963440.05912949255050.03528096423852.042049349790.2662619548321.7883802121621.9909049911-63.223608222190.8326394866
148.332526571873.8723704501-3.961381914368.150510754360.403854860924.06526707202-0.677106823983-0.967590508307-0.642168862985-0.5633407090781.21951654595-1.476191381311.09082555907-2.09324470668-0.4039877196221.350561707970.006145407292910.07816593887681.83934803610.3606536627561.3792278398534.6551537084-74.678477714784.3723942634
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 75 )AA0 - 751 - 76
22chain 'A' and (resid 76 through 164 )AA76 - 16477 - 165
33chain 'A' and (resid 165 through 272 )AA165 - 272166 - 273
44chain 'B' and (resid 0 through 75 )BC0 - 751 - 76
55chain 'B' and (resid 76 through 272 )BC76 - 27277 - 273
66chain 'C' and (resid 1 through 31 )CF1 - 311 - 31
77chain 'C' and (resid 32 through 47 )CF32 - 4732 - 47
88chain 'C' and (resid 48 through 67 )CF48 - 6748 - 67
99chain 'C' and (resid 68 through 83 )CF68 - 8368 - 83
1010chain 'C' and (resid 84 through 164 )CF84 - 16484 - 164
1111chain 'C' and (resid 165 through 189 )CF165 - 189165 - 189
1212chain 'C' and (resid 190 through 207 )CF190 - 207190 - 207
1313chain 'C' and (resid 208 through 250 )CF208 - 250208 - 250
1414chain 'C' and (resid 251 through 272 )CF251 - 272251 - 272

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