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- PDB-3ftf: Crystal structure of A. aeolicus KsgA in complex with RNA and SAH -

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Basic information

Entry
Database: PDB / ID: 3ftf
TitleCrystal structure of A. aeolicus KsgA in complex with RNA and SAH
Components
  • 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*CP*GP*GP*UP*U)-3'
  • Dimethyladenosine transferase
KeywordsTRANSFERASE/RNA / KsgA / Rossmann-like fold / RNA Methyltransferase / MTase / RNA / Antibiotic resistance / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine / Transferase / TRANSFERASE-RNA COMPLEX
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 methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / 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 methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / 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
: / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethyladenosine transferase
C: 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*CP*GP*GP*UP*U)-3'
D: 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*CP*GP*GP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1345
Polymers42,7113
Non-polymers4242
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-23.6 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.130, 58.074, 68.981
Angle α, β, γ (deg.)90.0, 109.82, 90.0
Int Tables number4
Space group name H-MP1211
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: RNA chain 5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*CP*GP*GP*UP*U)-3'


Mass: 7113.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 16S rRNA
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 35.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2 M KF, 40% MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KF11
2MPD11
3KF12
4MPD12

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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: Oct 6, 2007 / 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: 2.78→30 Å / Num. all: 6848 / Num. obs: 6848 / % possible obs: 84.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.4 / Num. unique all: 410 / Rsym value: 0.342 / % possible all: 49.9

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Processing

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

3ftc


Resolution: 2.8→28.33 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: 1. THE EFFECTIVE RESOLUTION FOR THIS STRUCTURE IS 3.05 ANGSTROM, AT WHICH THE COMPLETENESS OF X-RAY DATA > 93% AND THE OBSERVABLE DATA > 70% FOR HIGHEST RESOLUTION SHELL. 2. HYDROGENS HAVE ...Details: 1. THE EFFECTIVE RESOLUTION FOR THIS STRUCTURE IS 3.05 ANGSTROM, AT WHICH THE COMPLETENESS OF X-RAY DATA > 93% AND THE OBSERVABLE DATA > 70% FOR HIGHEST RESOLUTION SHELL. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28795 307 4.5 %RANDOM
Rwork0.23885 ---
obs0.2411 6491 85.1 %-
all-6776 --
Displacement parametersBiso mean: 28.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 948 27 36 2996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.171
X-RAY DIFFRACTIONr_bond_refined_d0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2.8-3.01620.3554870.22180056
3.0162-3.31930.31021160.1844107875
3.3193-3.79870.25681460.1725134194
3.7987-4.78220.23661580.1615144799
4.7822-28.32670.25081640.1934145699

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