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

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Basic information

Entry
Database: PDB / ID: 7uuj
TitleCrystal structure of aminoglycoside resistance enzyme ApmA, complex with gentamicin
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 / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology: / Trimeric LpxA-like superfamily / transferase activity / metal ion binding / Chem-LLL / Aminocyclitol acetyltransferase ApmA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 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: To Be Published
Title: Crystal structure of aminoglycoside resistance enzyme ApmA, complex with gentamicin
Authors: Stogios, P.J.
History
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords
Item: _audit_author.name / _pdbx_SG_project.full_name_of_center ..._audit_author.name / _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text
Revision 1.2Oct 25, 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: Aminocyclitol acetyltransferase ApmA
B: Aminocyclitol acetyltransferase ApmA
C: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,65413
Polymers93,9733
Non-polymers1,68110
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-62 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.763, 107.128, 137.079
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, 3 molecules ABC

#1: Protein Aminocyclitol acetyltransferase ApmA


Mass: 31324.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: apmA / Plasmid: PET19BTEV / Details (production host): 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 , 5 types, 829 molecules

#2: Chemical ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H39N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 819 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium chloride dihydrate, 16% PEG3350, 2.5 mM gentamicin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 83620 / % possible obs: 96.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 27.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Net I/σ(I): 19.09
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1 / Num. unique obs: 3882 / CC1/2: 0.878 / Rpim(I) all: 0.376 / % possible all: 91

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Processing

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

7jm2


Resolution: 1.78→29.85 Å / SU ML: 0.2255 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1983 2.39 %Random
Rwork0.1715 81034 --
obs0.1727 83017 95.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.21 Å2
Refinement stepCycle: LAST / Resolution: 1.78→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 112 819 7503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126889
X-RAY DIFFRACTIONf_angle_d1.10959354
X-RAY DIFFRACTIONf_chiral_restr0.07641021
X-RAY DIFFRACTIONf_plane_restr0.00811205
X-RAY DIFFRACTIONf_dihedral_angle_d15.17782554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.36881290.31695270X-RAY DIFFRACTION88.31
1.82-1.870.33711370.26615640X-RAY DIFFRACTION93.8
1.87-1.930.25411400.21985719X-RAY DIFFRACTION95.52
1.93-1.990.27281350.19355528X-RAY DIFFRACTION92.43
1.99-2.060.21251370.18845662X-RAY DIFFRACTION94.17
2.06-2.140.22411420.17685824X-RAY DIFFRACTION97.15
2.14-2.240.2411430.16765888X-RAY DIFFRACTION97.57
2.24-2.360.20411450.16625858X-RAY DIFFRACTION97.34
2.36-2.50.26391370.175585X-RAY DIFFRACTION92.63
2.5-2.70.24451460.17145948X-RAY DIFFRACTION98.32
2.7-2.970.23891470.16945988X-RAY DIFFRACTION98.4
2.97-3.40.2181440.16165877X-RAY DIFFRACTION95.95
3.4-4.280.17261510.14296110X-RAY DIFFRACTION99.05
4.28-29.850.21041500.17456137X-RAY DIFFRACTION96.03
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)
14.926873616411.01759830793-0.8710250033054.61595542136-0.4945664699395.34093013274-0.01144915771040.082590452059-0.0318458492945-0.0175402402986-0.07564967035430.408874868650.0475690788554-0.08836083809350.06740024984410.1418074137650.0223134244688-0.02382811103470.138972870356-0.04734741774810.261373673186-6.61184307144-17.8927446453-25.4680731569
20.7737707100290.880794689728-0.2093721953715.61849673987-1.349295274620.315961554835-0.07004868466950.09013068090820.0566191245879-0.1386654340770.017496807236-0.1095661576960.02310288970820.01518273789270.06082122828610.16679146840.006084040744450.008853880853750.168682981007-0.009458076067330.16256455139219.0310570101-4.21057856142-27.2275982617
32.58963408031-0.6541171305450.01389944411823.91714332128-0.8845481912941.92313647064-0.100095827948-0.08077395983520.02080566816780.23327675923-0.0489332144409-0.518553008024-0.06992103051080.1885139860740.1214990471620.1668853755080.0264915379756-0.02401386585170.1819861521290.01436928902250.18369931124227.093148269-23.1308182839-17.4721408521
43.688644039520.9381221402151.613722846952.132079354221.081081409063.50355047284-0.05005505965250.1039125198340.144350330685-0.02643734872690.02493038397850.09841058810040.0850874017668-0.1531680464520.01734996945180.1565702001590.018288726328-0.0004672381697060.1705401811540.06291163886150.225422106271-2.2879284668312.2888237677-29.3782362858
51.569034577210.485082489577-1.898942793770.615638657684-0.8195184660533.199773478560.0182319559451-0.2934492287840.2068683236140.069505418666-0.02596523134290.00169356471779-0.1500145718960.3125400091060.01328250978610.168806520688-1.5467134944E-5-0.03069945165230.247961326904-0.03206757680970.24482925346518.65459662916.5131399326-10.6955671312
61.116323268774.082854063045.77678973642.000003863262.000005207972.000003462296.35575815154-3.53222976179-1.3479601387-0.0753943833096-0.04352036321448.078924036629.90871001933-7.10626129903-6.311977477670.80499950339-0.236227585537-0.146491207410.8763637789150.2403252578781.1789037369338.533863630732.7645092345-26.1422579165
76.079567185071.521188785011.427541796487.336920092653.518304191266.27228847028-0.203370335287-0.460665947686-0.9604875182580.5048887357020.196238642658-0.03010049015431.10330299716-0.1793245246570.03761271451840.386363477633-0.006038931878930.006618692250820.3166403398310.05279355597360.336039985902-11.2859699988-7.683726455771.13704306427
83.934601037311.357714846280.2605764576036.95568338287-0.6468188984575.13835684584-0.00117929116042-0.05304014498380.0121485858504-0.187336620051-0.02075044911240.258329815063-0.0411732430053-0.2743748072580.009172756556660.1630268309880.0520550465883-0.04455715451620.2202541987410.005679136124220.190252931941-16.0514030081.8910808536-7.72250626803
95.33412184487-2.375819345142.736662340982.03499373321-2.161806380465.5531872594-0.30027063784-0.04119552427150.1586924456050.1113424359590.0681874682075-0.007171302663260.046330780856-0.04476971391030.2220341791760.1729690366550.001919452557910.0173165937870.187654233509-0.02728347800890.173991392806-5.816293095380.8641768499781.38984877811
103.644439671460.6640640632110.4648240130369.289717976711.972190383921.21314170076-0.1791870859580.16721705043-0.039444541549-0.3663203338580.149799669215-0.02739533946060.1911165210260.09899089308230.04153912713750.2134304615170.05552409145480.02227598109260.2179796124910.01324024264990.1180211906687.2328169483-8.045105295480.332989982156
110.675455548319-1.00509837718-0.6412292694024.612292801943.769345003823.13254621915-0.229240111087-0.238903633123-0.1152179432950.4851158211260.2353788250720.1352088681220.3343403603620.121026028362-0.01917307230580.2652754834130.08481988988870.0318238461790.2639239118640.04595853391490.19646014366614.8119228121-19.7979466217-2.60963407237
121.056398763310.4216295346181.050684862631.136603350.09656141216542.51118171201-0.322777908705-1.00361703020.3344833115390.4018660565630.382593811115-0.1674702569460.1826820881790.590781374476-0.05421833026050.3499555595980.168093653381-0.04421237856860.560528371734-0.08907687232170.28443443925913.35562394771.9163644355217.1091096405
137.087337311733.41854834194-6.083667612193.61849386819-1.828983620345.994523297-9.555464572365.35289294571-4.88400462618-13.20417693819.47258029934-6.59101107434-2.11289303622-0.4766401380740.09374967754870.6865924977990.1225758435030.01784294691381.32902909581-0.02663957451540.63895919516613.64422862453.0102250317633.1823657756
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 78 )AA1 - 781 - 78
22chain 'A' and (resid 79 through 189 )AA79 - 18979 - 189
33chain 'A' and (resid 190 through 272 )AA190 - 272190 - 272
44chain 'B' and (resid 0 through 97 )BE0 - 971 - 98
55chain 'B' and (resid 98 through 272 )BE98 - 27299 - 273
66chain 'B' and (resid 273 through 273 )BE273274
77chain 'C' and (resid -1 through 12 )CH-1 - 121 - 14
88chain 'C' and (resid 13 through 63 )CH13 - 6315 - 65
99chain 'C' and (resid 64 through 104 )CH64 - 10466 - 106
1010chain 'C' and (resid 105 through 132 )CH105 - 132107 - 134
1111chain 'C' and (resid 133 through 207 )CH133 - 207135 - 209
1212chain 'C' and (resid 208 through 272 )CH208 - 272210 - 274
1313chain 'C' and (resid 273 through 273 )CH273275

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