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- PDB-7uul: Crystal structure of aminoglycoside resistance enzyme ApmA, compl... -

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Basic information

Entry
Database: PDB / ID: 7uul
TitleCrystal structure of aminoglycoside resistance enzyme ApmA, complex with kanamycin B 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 / Chem-9CS / COENZYME A / Aminocyclitol acetyltransferase ApmA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsStogios, P.J. / Evdokimova, E. / 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

Downloads & links

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Assembly

Deposited unit
A: Aminocyclitol acetyltransferase ApmA
B: Aminocyclitol acetyltransferase ApmA
C: Aminocyclitol acetyltransferase ApmA
D: Aminocyclitol acetyltransferase ApmA
E: Aminocyclitol acetyltransferase ApmA
F: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,20537
Polymers187,9466
Non-polymers8,25931
Water32,9491829
1
A: Aminocyclitol acetyltransferase ApmA
B: Aminocyclitol acetyltransferase ApmA
D: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,52419
Polymers93,9733
Non-polymers4,55116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17570 Å2
ΔGint-108 kcal/mol
Surface area33410 Å2
MethodPISA
2
C: Aminocyclitol acetyltransferase ApmA
F: Aminocyclitol acetyltransferase ApmA
hetero molecules

E: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,68118
Polymers93,9733
Non-polymers3,70815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area16410 Å2
ΔGint-54 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.093, 131.685, 157.915
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

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Aminocyclitol acetyltransferase ApmA


Mass: 31324.320 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 1860 molecules

#2: Chemical
ChemComp-9CS / (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE / Kanamycin B / Bekanamycin


Mass: 483.514 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H37N5O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1829 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M litium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350, 5 mM kanamycin B

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→29.47 Å / Num. obs: 99115 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Net I/σ(I): 22.2
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4910 / CC1/2: 0.889 / Rpim(I) all: 0.436 / % possible all: 99.4

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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: 2.26→29.47 Å / SU ML: 0.2593 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 3281 2.05 %RANDOM
Rwork0.1722 156748 --
obs0.1734 96912 83.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.58 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13187 0 524 1829 15540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011614073
X-RAY DIFFRACTIONf_angle_d1.419219133
X-RAY DIFFRACTIONf_chiral_restr0.05952083
X-RAY DIFFRACTIONf_plane_restr0.00962422
X-RAY DIFFRACTIONf_dihedral_angle_d16.91065090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.273630.27453005X-RAY DIFFRACTION36.72
2.29-2.320.3221770.25043703X-RAY DIFFRACTION45.5
2.32-2.360.2451900.23734193X-RAY DIFFRACTION50.8
2.36-2.40.2952910.21494491X-RAY DIFFRACTION55.08
2.4-2.450.21931020.20694783X-RAY DIFFRACTION58.81
2.45-2.490.27631060.21265180X-RAY DIFFRACTION63.26
2.49-2.540.25481180.20285652X-RAY DIFFRACTION68.92
2.54-2.60.26281370.20196411X-RAY DIFFRACTION78.33
2.6-2.660.28391540.2117268X-RAY DIFFRACTION89.19
2.66-2.730.29721630.21437774X-RAY DIFFRACTION94.7
2.73-2.80.30491640.2127989X-RAY DIFFRACTION97.59
2.8-2.880.25931650.21088060X-RAY DIFFRACTION98.5
2.88-2.980.28271720.1978103X-RAY DIFFRACTION98.58
2.98-3.080.32341710.19717981X-RAY DIFFRACTION98.35
3.08-3.20.29961700.19167989X-RAY DIFFRACTION97.86
3.2-3.350.2581630.18037998X-RAY DIFFRACTION97.87
3.35-3.530.20411680.16337980X-RAY DIFFRACTION97.02
3.53-3.750.20051660.15067861X-RAY DIFFRACTION96.35
3.75-4.040.19331690.13597895X-RAY DIFFRACTION96.83
4.04-4.440.16531690.13248005X-RAY DIFFRACTION97.96
4.44-5.080.19551680.12838141X-RAY DIFFRACTION99.33
5.08-6.390.2191690.15748138X-RAY DIFFRACTION99.59
6.39-29.470.1961660.17238148X-RAY DIFFRACTION99.55
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)
13.59741462097-1.55807063257-1.02808393933.68751797681-1.098925793714.109813844570.1384824966540.131014155814-0.377519638898-0.0456910492814-0.227502903670.239332419142-0.0683584487149-0.1567886412080.06714908218460.182604471587-0.0331560203215-0.02360803328050.24100567012-0.08549385430440.280371005537.52483275555-31.754651597-29.9137486341
23.0158201697-0.05578782459831.339426595310.129318249670.2426075271061.573773865670.0118456136928-0.2967984583880.2828450064390.0937779094943-0.0891596781174-0.0356472726014-0.157561128222-0.1457441335540.09474755043420.220187101496-0.04677923613640.0145339967170.18429047324-0.02547406959550.22155906027429.7189594999-12.4038964581-32.0480593404
35.56250355024-0.3028465115981.560187804572.87412424696-0.3572320820372.897054785770.04546699729510.6275081957990.367257173359-0.150070939825-0.1373516706290.115123218484-0.356878528268-0.1463025297160.1043320137510.2726311638440.05999178038470.05084208530670.2373742158370.02420220619730.19379979997718.6036650857-6.11917388456-52.8497100162
45.15237697321-0.6425278522950.2695590080464.81003079899-0.1072641775364.99381412942-0.0192417977634-0.181383018392-0.2206183704810.3517603997670.00838877998163-0.3181520559720.2596218650060.11383091670.01511457814240.261539292959-0.0495182810049-0.02823702665510.158878419994-0.005609476972430.25158847089526.5493639891-53.9725180615-34.6688967536
53.28843445156-1.24670461897-0.5261561190343.9704829576-2.20374078021.904908150890.0731294238850.123842454248-0.3140207914250.078669137626-0.0872178156480.41105163010.154554039525-0.293528122564-0.0001352680698250.293325328493-0.09291962978310.01489564216110.248273180627-0.03122482822370.17075945957530.6797834435-40.5264098416-49.3441659488
62.95835844908-2.02662530784-0.3648729775292.386861315030.4056755459460.3916665558190.2507481581390.408034616293-0.0137673966778-0.249831829474-0.294192732550.1083804684050.0372105620845-0.170759221380.03782742116070.257687658232-0.01724626727250.00322392472810.2857791369860.000458636616940.13034573785528.8335346479-25.9360972602-57.3393783366
76.190701034590.1275629144490.1335480699433.972536129250.7493614793243.57504641338-0.1309555727520.584242504081-0.699061640712-0.559576572219-0.123886866958-0.4626923558690.8739163615430.1080991547260.2906605640620.5781221736020.107886025070.1013802927510.339140528317-0.05927201753350.33216921009249.4189166117-49.0822217061-62.2387157838
81.95642937767-0.1285572738880.09419371735271.705389044620.5396699368763.244742319920.05001019154150.168392374045-0.0657237207391-0.0057715870781-0.0684207446536-0.14460496320.1514787439940.2789756713780.007176965591140.1321209077310.0429680013297-0.002251041702880.2734799968580.07239300348290.31952003312324.4199788001-65.5769842467-71.3480921105
92.67281544532.048474577570.4847619034532.974800312860.1535634708531.35982550333-0.127885149210.0602079599565-0.0856035192406-0.2422886003510.0555390443083-0.0455918418868-0.0293497293553-0.01353309264480.06695862982710.1856320943160.0326086375524-0.01387065236450.2497789159980.02080013883030.1594455540330.235168184509-59.2489924414-88.5718195241
103.405097933150.656714500499-0.8705747063825.32658454562-0.2480792872542.61012522206-0.1972225689750.630168779010.258048575489-0.224912183276-0.0258257827257-0.485271617083-0.5382903687490.6398234112480.2313466349290.356282243117-0.152823868694-0.01163844037910.5215096282830.1186874127010.31842344213620.5976499274-39.1592626155-93.2669220999
115.35610047752-0.723788837944-0.03165783694422.60383558114-0.6770155971473.614963227250.00652661659749-0.780112595088-0.02731923344490.305718246586-0.08711067906490.1012936085090.250519821395-0.2713434863160.09447099269580.340184607491-0.121863352466-0.03171538614130.397234511411-0.04465517709530.23244665570632.9381479563-34.3441834334-13.5700021564
120.6996649837470.160705521160.03908998094211.74319500351.00093108652.001581060470.0575621344969-0.1321163450860.06055235988320.06768504015820.0206662987924-0.3562649190930.09693016256260.211727231283-0.06856346722210.150211207989-0.0197941208963-0.006574999827380.2394035698550.01299079776350.28849848756552.2584018928-25.7929767763-33.0889460012
132.88132053578-0.5540261429961.3003205674.160634974331.509407288795.30702674472-0.0613899496792-0.0603857299864-0.1702881041670.3101952673710.01694831078230.2353289695360.1189263950390.09779725679590.03782062638910.1569808780430.01432076172440.04068944329930.199938739707-0.01504524606360.221705930732-0.787875133293-17.6501422332-11.4512902791
140.652332961868-0.5171534231810.6460402404431.83565724616-0.6574674709882.36959109285-0.05815544599160.2063501002730.1291534932550.00991478945137-0.00510427466935-0.279769579165-0.03806680004440.5858769731730.09697789874410.135922102357-0.0562271124777-0.006788902308930.4509099526-0.03038389624120.31599232823819.28842561042.04161067281-6.1448300212
155.55291054887-0.166273661377-0.2640086624713.0586170731.348757458864.24275555212-0.0383966032694-0.28998967845-0.03218057349690.247352738573-0.05980169214590.1589035161260.218126789459-0.1630991540940.07008994120710.265132516171-0.0469088613996-6.1582914595E-50.1649341203530.01434791702080.176129503577.89388674319-64.5746037184-46.1419376974
169.518454397911.2577910188-2.882735962697.38719679678-6.282463833267.1194934693-0.0157845488929-0.0700389187510.004750344351710.395261844159-0.236539246983-0.050173495756-0.5985575122060.6196325227650.2276815994720.295542699855-0.0293247670924-0.09168624429380.265050981303-0.002502943630560.1594783405185.17079515101-50.7702921894-52.8412867187
171.490938889810.693217733807-1.342826522940.981434688439-0.8154524179883.671039246510.0443049293839-0.08284118928530.2525919466410.213960903054-0.0777355546451-0.0352959489811-0.5819126877170.2258926507380.02951204302730.350551000820.0233138454089-0.08516207366640.203136931473-0.01152669448330.2437033263646.67447716802-41.7279419464-68.6567852551
181.629033455920.155982609441-0.1196191112792.022951190561.028321147790.74968430465-0.0143802776253-0.2272306563390.5436060723250.557903833471-0.007460392506860.417881522414-1.15686054099-0.91796662582-0.004902816729620.771138028640.3205917932310.02368201710720.563712532882-0.123187006130.443642526805-14.1447943131-37.6652478927-54.632253498
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 78 )AA0 - 781 - 79
22chain 'A' and (resid 79 through 207 )AA79 - 20780 - 208
33chain 'A' and (resid 208 through 273 )AA208 - 273209 - 274
44chain 'B' and (resid -1 through 78 )BD-1 - 781 - 80
55chain 'B' and (resid 79 through 132 )BD79 - 13281 - 134
66chain 'B' and (resid 133 through 234 )BD133 - 234135 - 236
77chain 'B' and (resid 235 through 273 )BD235 - 273237 - 275
88chain 'C' and (resid 1 through 93 )CG1 - 931 - 93
99chain 'C' and (resid 94 through 234 )CG94 - 23494 - 234
1010chain 'C' and (resid 235 through 273 )CG235 - 273235 - 273
1111chain 'D' and (resid 0 through 93 )DI0 - 931 - 94
1212chain 'D' and (resid 94 through 274 )DI94 - 27495 - 275
1313chain 'E' and (resid -1 through 93 )EL-1 - 931 - 95
1414chain 'E' and (resid 94 through 274 )EL94 - 27496 - 276
1515chain 'F' and (resid -1 through 78 )FO-1 - 781 - 80
1616chain 'F' and (resid 79 through 97 )FO79 - 9781 - 99
1717chain 'F' and (resid 98 through 207 )FO98 - 207100 - 209
1818chain 'F' and (resid 208 through 273 )FO208 - 273210 - 275

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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