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

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Basic information

Entry
Database: PDB / ID: 6sxj
TitleCrystal structure of spectinomycin adenyltransferase AAD(9) from Enterococcus faecialis
ComponentsStreptomycin 3''-adenylyltransferase
KeywordsTRANSFERASE / nucleotidyltransferase / antibiotic resistance
Function / homologyAdenylyltransferase AadA, C-terminal domain / Aminoglycoside adenylyltransferase, C-terminal domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / response to antibiotic / ATP binding / Spectinomycin 9-adenylyltransferase
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / Item: _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)30,9662
Polymers30,8731
Non-polymers921
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.971, 103.971, 61.019
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.53 % / 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 aminoacid, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.1→37 Å / Num. obs: 18995 / % possible obs: 99 % / Redundancy: 13.7 % / Biso Wilson estimate: 51.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.058 / Net I/σ(I): 1.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1843 / CC1/2: 0.8 / Rpim(I) all: 0.4 / % possible all: 97

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Processing

Software
NameVersionClassification
Coot1.15.2_3472model building
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4A

5g4a


Resolution: 2.1→36.98 Å / SU ML: 0.296 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3315
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 958 5.05 %Random selection
Rwork0.2298 ---
obs0.2321 18983 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 6 16 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542087
X-RAY DIFFRACTIONf_angle_d0.72972819
X-RAY DIFFRACTIONf_chiral_restr0.0436318
X-RAY DIFFRACTIONf_plane_restr0.0047361
X-RAY DIFFRACTIONf_dihedral_angle_d2.68321296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.210.3766152250197.75
2.21-2.350.3969133254298.2
2.35-2.530.3326111256899.15
2.53-2.790.3548135257799.78
2.79-3.190.3564146259499.78
3.19-4.020.2736133259899.96
4.020.21751480.1815264599.86

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