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- PDB-7uy4: Aminoglycoside-modifying enzyme ANT-3,9 in complex with spectinom... -

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Basic information

Entry
Database: PDB / ID: 7uy4
TitleAminoglycoside-modifying enzyme ANT-3,9 in complex with spectinomycin and AMP-PNP
ComponentsAminoglycoside (3'') (9) adenylyltransferase
KeywordsTRANSFERASE / Antibiotic resistance / Drug modifying enzymes / aminoglycoside / spectinonmycin / streptomycin / AMEs / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding
Similarity search - Function
Adenylyltransferase AadA/Aad9 / Adenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / SPECTINOMYCIN / Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsReeve, S.M. / Lee, R.E. / Das, N. / Jayaraman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Characterization of the spectinomycin deactivating enzyme ANT-3,9
Authors: Das, N. / Reeve, S.M. / Lee, R.E.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Aminoglycoside (3'') (9) adenylyltransferase
B: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,24310
Polymers57,4332
Non-polymers1,8108
Water6,341352
1
A: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6225
Polymers28,7161
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoglycoside (3'') (9) adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6225
Polymers28,7161
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.043, 106.958, 114.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 256 / Label seq-ID: 1 - 256

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aminoglycoside (3'') (9) adenylyltransferase


Mass: 28716.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aadA1 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W8FS12, streptomycin 3''-adenylyltransferase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SMI / SPECTINOMYCIN / (2R,4aR,5aR,6S,7S,8R,9S,9aR,10aS)-2-methyl-6,8-bis(methylamino)hexahydro-2H-pyrano[2,3-b][1,4]benzodioxine-4,4,4a,7,9(3H,10aH)-pentol


Mass: 350.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, pH 6.2 0.2M MgCl2 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 40924 / % possible obs: 98.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 17.1
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 1.067 / Num. unique obs: 2573

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xxq

6xxq


Resolution: 1.98→48.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.989 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22147 2158 5 %RANDOM
Rwork0.17845 ---
obs0.1806 40924 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0 Å2
2---0.94 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: 1 / Resolution: 1.98→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 114 352 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153992
X-RAY DIFFRACTIONr_angle_refined_deg1.711.665848
X-RAY DIFFRACTIONr_angle_other_deg1.3731.5989189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72622.925212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50815661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4171526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02887
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4594.7452081
X-RAY DIFFRACTIONr_mcbond_other4.4564.7432080
X-RAY DIFFRACTIONr_mcangle_it5.5557.1032605
X-RAY DIFFRACTIONr_mcangle_other5.5557.1052606
X-RAY DIFFRACTIONr_scbond_it5.1065.0392164
X-RAY DIFFRACTIONr_scbond_other5.1055.0392165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7047.4263242
X-RAY DIFFRACTIONr_long_range_B_refined9.26159.2045257
X-RAY DIFFRACTIONr_long_range_B_other9.26159.1145245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7967 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.98→2.029 Å
RfactorNum. reflection% reflection
Rfree0.262 156 -
Rwork0.185 2573 -
obs--86.12 %

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