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- PDB-6xz0: Crystal structure of spectinomycin adenyltransferase AAD(9) from ... -

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Basic information

Entry
Database: PDB / ID: 6xz0
TitleCrystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis with spectinomycin
ComponentsStreptomycin 3''-adenylyltransferase
KeywordsTRANSFERASE / nucleotidyltransferase / antibiotic resistance
Function / homology
Function and homology information


nucleotidyltransferase activity / response to antibiotic / ATP binding
Similarity search - Function
Adenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
SPECTINOMYCIN / Spectinomycin 9-adenylyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKanchugal P, S. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Swedish Research Council2016-06889 Sweden
CitationJournal: Antimicrob.Agents Chemother. / Year: 2020
Title: Structural Recognition of Spectinomycin by Resistance Enzyme ANT(9) from Enterococcus faecalis.
Authors: Kanchugal P, S. / Selmer, M.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptomycin 3''-adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2062
Polymers30,8731
Non-polymers3321
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-2 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.561, 99.561, 61.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Streptomycin 3''-adenylyltransferase / AAD(9)


Mass: 30873.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: spc, aad9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q07448, streptomycin 3''-adenylyltransferase
#2: Chemical ChemComp-SCM / SPECTINOMYCIN / ACTINOSPECTACIN / ESPECTINOMICINA / CHX-3101


Mass: 332.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N2O7 / Feature type: SUBJECT OF INVESTIGATION
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: 2.46 Å3/Da / Density % sol: 60 % / Description: Hexagonal prism-shaped
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M of each alcohol (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), ...Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M of each alcohol (0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), 0.1 M bicine/Trizma base pH 8.5) were soaked with 10 mM ATP, 10 mM magnesium and spectinomycin powder for 30 seconds

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→49.8 Å / Num. obs: 7509 / % possible obs: 99.6 % / Redundancy: 22.9 % / Biso Wilson estimate: 69.18 Å2 / CC1/2: 0.9 / CC star: 1 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.1 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 751 / CC1/2: 0.9 / CC star: 0.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDS1.15.2_3472data reduction
Aimless1.15.2_3472data scaling
PHASERphasing
Cootmodel building
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SXJ

6sxj


Resolution: 2.8→49.78 Å / SU ML: 0.5886 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.7612
RfactorNum. reflection% reflection
Rfree0.3026 385 5.15 %
Rwork0.245 --
obs0.2486 7480 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 75.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 23 0 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292108
X-RAY DIFFRACTIONf_angle_d0.63412856
X-RAY DIFFRACTIONf_chiral_restr0.0474326
X-RAY DIFFRACTIONf_plane_restr0.0042363
X-RAY DIFFRACTIONf_dihedral_angle_d2.9031309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.48171260.34812364X-RAY DIFFRACTION99.56
3.21-4.040.33961240.26712344X-RAY DIFFRACTION99.44
4.04-49.780.24911350.21022387X-RAY DIFFRACTION99.72

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