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

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Basic information

Entry
Database: PDB / ID: 7uum
TitleCrystal structure of aminoglycoside resistance enzyme ApmA, complex with paromomycin 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 / PAROMOMYCIN / Aminocyclitol acetyltransferase ApmA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsStogios, P.J. / Evdokimova, E. / Osipiuk, J. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8004
Polymers31,3241
Non-polymers1,4753
Water95553
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)98,39912
Polymers93,9733
Non-polymers4,4269
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area17780 Å2
ΔGint-63 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.748, 133.748, 133.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-442-

HOH

31A-453-

HOH

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Components

#1: Protein Aminocyclitol acetyltransferase ApmA


Mass: 31324.320 Da / Num. of mol.: 1
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M litihium sulfate, 0.1 M Tris pH 8.5, 23% PEG3350, 14 mM paromomycin

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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: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 11364 / % possible obs: 100 % / Redundancy: 30.1 % / Biso Wilson estimate: 41.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.036 / Net I/σ(I): 20.21
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.791 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 548 / CC1/2: 0.527 / Rpim(I) all: 0.548 / % possible all: 100

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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: 2.74→35.75 Å / SU ML: 0.3119 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 940 4.99 %RANDOM
Rwork0.223 17892 --
obs0.2243 10423 92.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.3 Å2
Refinement stepCycle: LAST / Resolution: 2.74→35.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 96 53 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282348
X-RAY DIFFRACTIONf_angle_d0.72533194
X-RAY DIFFRACTIONf_chiral_restr0.0513350
X-RAY DIFFRACTIONf_plane_restr0.0026402
X-RAY DIFFRACTIONf_dihedral_angle_d18.3166848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.880.3031710.33731335X-RAY DIFFRACTION48.17
2.88-3.060.40271420.30342746X-RAY DIFFRACTION98.53
3.06-3.290.25731440.27412742X-RAY DIFFRACTION99.97
3.3-3.630.27971460.24052776X-RAY DIFFRACTION99.46
3.63-4.150.25781420.21592745X-RAY DIFFRACTION99.38
4.15-5.220.18991490.17922762X-RAY DIFFRACTION99.97
5.23-35.750.21011460.18552786X-RAY DIFFRACTION99.8
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)
18.16885865487-1.056884853141.993010213171.3390677995-0.817592687182.47897007330.381438514989-0.804761042441-0.162243042310.1314027165-0.04721912209680.1269560871920.00455081764332-0.19683950321-0.2137395272470.346054251887-0.07256138415090.08571893151810.298502340364-0.03716979265880.281812767675-23.5123855952-10.69522950067.9180669456
22.937230861510.823816588189-0.4268987041764.16989007867-0.5171312587933.12345947559-0.01452562488870.2046155388640.33479570599-0.1121205134750.1618352715030.201478187693-0.254695850085-0.260525840248-0.1327976104990.2061578063570.07569054274020.07215910788920.2721064159460.02016300870220.18950178589-26.3928691974-6.67146021367-5.65860080703
33.119999914880.8873464519352.594121272161.546733868530.1169139466862.60554720184-0.1161278243140.01140205833680.05718504031630.1823449997060.17094088-0.0232935144484-0.0873668315490.0995181934009-0.07217882609620.3835622991180.02011361580620.04340902730550.283969074229-0.05519421298330.236940165643-12.8814237711-2.8073102420611.3283909519
42.51599998989-1.869121031120.4683281047463.973993261581.401660481812.76179278908-0.2503047131-0.906827216407-0.39986792330.997520522140.1352015459640.0935941458590.3024484821910.3988585183110.1480981826540.6481757589780.103925244082-0.0861502936540.6902573021830.165143538150.3391081276659.48797086346-20.198522057417.6540582847
53.481901596050.319620789922-0.8593707152331.996821134770.6811610399761.760012115180.0377969959269-0.6500561081560.002833529687790.4418714927590.190681446552-0.2583446177510.02046872162660.498577955524-0.1947657222860.4764872669180.00769880843336-0.1127259307620.473693116755-0.09988893056980.275472049451-1.88726934671-0.98066176003519.1583791512
62.3137768383-0.469597525148-2.662024562393.182630707292.275808816765.533836599260.0887350982263-0.6031248874250.7387526897290.5329193267870.0175422668985-0.209738221441-0.4488339977740.759702765516-0.09474482314980.749143962588-0.149104363626-0.136279790880.519852067157-0.1744178477780.486848717509-0.52473784197511.462199605819.9623737007
70.408609042032-0.2237188165080.05227857460222.881451544310.6139766210582.16516502589-0.0408026002281-0.7593563263680.6347471950390.7074548702010.09527080671670.320448929482-0.735742761612-0.544874077020.01341112445360.8275832263430.1860081902670.150841857230.758295309748-0.245193742090.595582064103-21.397743844916.153374813123.7094223348
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 12 )-1 - 121 - 14
22chain 'A' and (resid 13 through 78 )13 - 7815 - 80
33chain 'A' and (resid 79 through 132 )79 - 13281 - 134
44chain 'A' and (resid 133 through 163 )133 - 163135 - 165
55chain 'A' and (resid 164 through 207 )164 - 207166 - 209
66chain 'A' and (resid 208 through 234 )208 - 234210 - 236
77chain 'A' and (resid 235 through 272 )235 - 272237 - 274

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