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PDB | 3FUW | T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space ...

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Internal ID
64025
PDB Entry ID
3FUW
Title
T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121
Authors
Demirci, H.,Belardinelli, R.,Seri, E.,Gregory, S.T.,Gualerzi, C.,Dahlberg, A.E.,Jogl, G.
Primary Citation
AuthorsDemirci, H., Belardinelli, R., Seri, E., Gregory, S.T., Gualerzi, C., Dahlberg, A.E., Jogl, G.
TitleStructural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
JournalJ.Mol.Biol., v.388, pp.271 - 282, 2009
AbstractView
Pubmed19285505
DOI10.1016/j.jmb.2009.02.066
 
History
Deposition: 2009-01-14Release: 2009-03-31Last Modified: 2011-07-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.560.1990.1970.235P 21 21 21
Unit Cell
Length [Å]a53.42b61.04c82.53
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Dimethyladenosine transferaseA2.1.1.-
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Thermus thermophilusEscherichia coli
Related PDB Entries
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
MTA5'-DEOXY-5'-METHYLTHIOADENOSINEC11H15N5O3S[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSFERASE
TextMethyltransferase, dimethyltransferase, dual-specific methyltransferase, 16S rRNA methyltransferase, translation, Antibiotic resistance, RNA-binding, rRNA processing, S-adenosyl-L-methionine, Transferase
 
Polymeric Molecules
Chain A
DescriptionDimethyladenosine transferase
Polymer typepolypeptide
Formula Weight29909.2
Source Methodgenetically manipulated
Entity NameS-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase, 16S rRNA dimethylase, High level kasugamycin resistance protein ksgA, Kasugamycin dimethyltransferase
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
MTA5'-DEOXY-5'-METHYLTHIOADENOSINEC11H15N5O3S297.331View
EC and Associated Pathways
ChainsIUBMBKEGG EnzymeMetaCycReactome
A2.1.1.-2.1.1.-2.1.1.-2.1.1.-
Natural/Genetically Modified Source
Scientific NameThermus thermophilus
Source Genusn/a
GeneksgA, TTHA0083
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21 (DE3)Star
Host Vector Typeplasmid
Host PlasmidpET26b
 
Crystallization Experiments
Methodmicrobatch technique under oil
PH8.5
Temperature277.0
Details17% w/v polyethylene glycol 4000, 85 mM HEPES-NaOH (pH 8.5), 8.5% v/v isopropanol and 15% v/v anhydrous glycerol, microbatch technique under oil, temperature 277K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
53.4261.0482.53
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 21
Diffraction Detector
DetectorCCD
TypeMAR CCD 130 mm
DetailsBent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
Collection Daten/a
 
Diffraction Radiation
MonochromatorBent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List0.9797
 
Diffraction Source
SourceSYNCHROTRON
TypeNSLS BEAMLINE X4C
SiteNSLS
BeamlineX4C
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)1.56
Resolution (Low)30.00
Number Reflections (All) n/a
Number Reflections (Observed)38372
Percent Possible (Observed)97.0
R Merge I (Observed)0.063
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy6.9
 
High Resolution Shell Details
Resolution(High)1.56
Resolution(Low)1.60
Percent Possible(All) 94.50
R Merge I(Observed)0.480
Mean I Over Sigma(Observed)2.6
R Sym I(Observed)n/a
Redundancy5.9
Num Unique Reflections(All)3682
 
Refinement Statistics
Structure Solution Methodn/a
Resolution (High)1.56
Resolution (Low)28.63
Cut-off Sigma (F)0.0
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)37953
Number of Reflections (R-Free) 1905
Percent Reflections (Observed)97.07
R-Factor (All)n/a
R-Factor (Observed)0.199
R-Work0.197
R-Free0.235
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value19.766
Anisotropic B[1][1]0.03
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.01
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-0.02
 
Resolution Shells
Shell Resol (High)1.56
Shell Resolution (Low)n/a
Number of Reflections (Observed)2524
Number of Reflections (R-Free)139
Number of Reflections (R-Work)2524
R-Factor (R-Work)0.227
R-Factor (R-Free)0.237
R-Free Errorn/a
Percent Reflections (Observed)94.63
 
RMS Deviations
First|Previous|1 of 2|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.010
r_angle_refined_deg1.341
r_dihedral_angle_1_deg5.878
r_dihedral_angle_2_deg26.111
r_dihedral_angle_3_deg12.950
r_dihedral_angle_4_deg16.162
r_chiral_restr0.084
r_gen_planes_refined0.007
r_mcbond_it0.590
r_mcangle_it1.025
First|Previous|1 of 2|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms2061
Nucleic Acid Atoms0
Heterogen Atoms20
Solvent Atoms335
 
Programs
Data CollectionHKL-2000
Data Reduction (intensity integration)HKL-2000
Data Reduction (data scaling)HKL-2000
Structure Solutionrigid body refinement REFMAC 5.5.0044
Structure RefinementREFMAC 5.5.0044
 
Software
Classificationrefinement
Software NameREFMAC5
Software Version 5.5.0044
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.006
 
Sequence Chain
A
Sequence
  1   MSKLASPQSV  RALLERHGLF  ADKRFGQNFL  VSEAHLRRIV  EAARPFTGPV  FEVGPGLGAL

 61   TRALLEAGAE  VTAIEKDLRL  RPVLEETLSG  LPVRLVFQDA  LLYPWEEVPQ  GSLLVANLPY

121   HIATPLVTRL  LKTGRFARLV  FLVQKEVAER  MTARPKTPAY  GVLTLRVAHH  AVAERLFDLP

181   PGAFFPPPKV  WSSLVRLTPT  GALDDPGLFR  LVEAAFGKRR  KTLLNALAAA  GYPKARVEEA

241   LRALGLPPRV  RAEELDLEAF  RRLREGLEGA  V