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- PDB-4cs6: Crystal structure of AadA - an aminoglycoside adenyltransferase -

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Basic information

Entry
Database: PDB / ID: 4cs6
TitleCrystal structure of AadA - an aminoglycoside adenyltransferase
ComponentsAMINOGLYCOSIDE ADENYLTRANSFERASE
KeywordsTRANSFERASE / AMINOGLYCOSIDE ADENYLTRANSFERASE / ANT(3'')
Function / homology
Function and homology information


streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding / metal ion 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
Aminoglycoside (3'') (9) adenylyltransferase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsChen, Y. / Nasvall, J. / Andersson, D.I. / Selmer, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of Aada from Salmonella Enterica: A Monomeric Aminoglycoside (3'')(9) Adenyltransferase.
Authors: Chen, Y. / Nasvall, J. / Wu, S. / Andersson, D.I. / Selmer, M.
History
DepositionMar 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMINOGLYCOSIDE ADENYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)29,5911
Polymers29,5911
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.658, 58.642, 104.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein AMINOGLYCOSIDE ADENYLTRANSFERASE


Mass: 29590.986 Da / Num. of mol.: 1
Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8ZPX9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0, 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionResolution: 2.5→39 Å / Num. obs: 10853 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 7.05 % / Biso Wilson estimate: 61.76 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.502→39.029 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 517 4.8 %
Rwork0.1935 --
obs0.1962 10816 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.3 Å2
Refinement stepCycle: LAST / Resolution: 2.502→39.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 0 30 2083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082103
X-RAY DIFFRACTIONf_angle_d1.2772876
X-RAY DIFFRACTIONf_dihedral_angle_d16.128769
X-RAY DIFFRACTIONf_chiral_restr0.084333
X-RAY DIFFRACTIONf_plane_restr0.006368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5019-2.75360.39241430.27542500X-RAY DIFFRACTION99
2.7536-3.15190.33781260.25052543X-RAY DIFFRACTION100
3.1519-3.97040.26841200.18982571X-RAY DIFFRACTION100
3.9704-39.0340.20011280.16982685X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.0012 Å / Origin y: 15.7438 Å / Origin z: 128.4074 Å
111213212223313233
T0.3167 Å20.0093 Å2-0.0735 Å2-0.3152 Å20.0479 Å2--0.3456 Å2
L3.8162 °20.4463 °2-1.9422 °2-2.5265 °2-1.2033 °2--4.6969 °2
S0.2259 Å °0.2458 Å °0.1288 Å °0.1132 Å °0.1811 Å °0.0898 Å °0.3438 Å °-0.2254 Å °-0.3659 Å °
Refinement TLS groupSelection details: ALL

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