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- PDB-3ftd: Crystal structure of A. aeolicus KsgA at 1.44-Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3ftd
TitleCrystal structure of A. aeolicus KsgA at 1.44-Angstrom resolution
ComponentsDimethyladenosine transferase
KeywordsTRANSFERASE / KsgA / Rossmann-like fold / RNA Methyltransferase / MTase / Antibiotic resistance / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytosol
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsTu, C. / Ji, X.
CitationJournal: Structure / Year: 2009
Title: Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase.
Authors: Tu, C. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethyladenosine transferase


Theoretical massNumber of molelcules
Total (without water)28,4841
Polymers28,4841
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.087, 57.383, 87.618
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly corresponds to the content of the asymmetric unit.

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Components

#1: Protein Dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase / High ...S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase / High level kasugamycin resistance protein ksgA / Kasugamycin dimethyltransferase


Mass: 28484.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: genomic DNA / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1816, ksgA / Plasmid: pBA1939 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: O67680, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG MME 5000, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2008 / Details: mirrors
RadiationMonochromator: Si(111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→30 Å / Num. all: 38594 / Num. obs: 38594 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.6
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3121 / Rsym value: 0.493 / % possible all: 66

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FTC

3ftc


Resolution: 1.44→28.691 Å / SU ML: 0.17 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 2000 5.31 %RANDOM
Rwork0.1588 ---
obs0.161 37676 94.48 %-
all-38594 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.043 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.74 Å21.5 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.026 Å0.02 Å
Luzzati d res low-3.4 Å
Luzzati sigma a0.3 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.44→28.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 277 2210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.906
X-RAY DIFFRACTIONf_dihedral_angle_d14.495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.44-1.47830.3355970.29291737173766
1.4783-1.51820.27271170.21952083208379
1.5182-1.56290.24281330.18572360236089
1.5629-1.61340.24381410.1662530253094
1.6134-1.6710.24331450.1532580258097
1.671-1.73790.19091470.14572635263599
1.7379-1.8170.25231490.14162645264599
1.817-1.91280.1971500.131926782678100
1.9128-2.03260.18911490.130526722672100
2.0326-2.18950.18141520.132226982698100
2.1895-2.40970.19581520.146927012701100
2.4097-2.75810.20481530.162727212721100
2.7581-3.4740.161530.156527512751100
3.474-28.69720.18531620.161928852885100

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