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- PDB-4jxj: Crystal Structure of Ribosomal RNA small subunit methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4jxj
TitleCrystal Structure of Ribosomal RNA small subunit methyltransferase A from Rickettsia bellii Determined by Iodide SAD Phasing
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / methyltransferase
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 / RNA binding / cytoplasm
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
IODIDE ION / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesRickettsia bellii (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Ribosomal RNA small subunit methyltransferase A from Rickettsia bellii Determined by Iodide SAD Phasing
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,31214
Polymers30,7271
Non-polymers1,58513
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.380, 81.330, 38.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase A / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 30727.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii (bacteria) / Strain: RML369-C / Gene: ksgA, RBE_0204, rsmA, YP_537374 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1RK29, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Wizard3/4(F6): 25% PEG-1500, 0.1M SPG Buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 27, 2013 / Details: Rigaku Varimax HF
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 222784 / Rmerge(I) obs: 0.09 / D res high: 2 Å / Num. obs: 32726 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.328.9467199.710.049
5.166.3288099.910.056
4.475.16101599.710.051
44.47118099.810.052
3.654130099.910.055
3.383.65141010010.063
3.163.38151110010.07
2.983.16159510010.087
2.832.98172999.910.104
2.72.83177210010.128
2.582.7187699.910.14
2.482.58196710010.173
2.392.48201710010.199
2.312.39210410010.209
2.242.31215310010.261
2.172.24226410010.289
2.112.17230599.910.322
2.052.11238799.410.314
22.05222692.710.37
ReflectionResolution: 2→50 Å / Num. all: 32923 / Num. obs: 32726 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.575 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.373.4577692226192.7
2.05-2.110.3144.55102212387199.4
2.11-2.170.3225.48129062305199.9
2.17-2.240.2897.311668222641100
2.24-2.310.2617.881594121531100
2.31-2.390.2099.571566221041100
2.39-2.480.1999.621506220171100
2.48-2.580.17310.91472119671100
2.58-2.70.1412.91141111876199.9
2.7-2.830.12813.591332517721100
2.83-2.980.10416.19129921729199.9
2.98-3.160.08719.091199915951100
3.16-3.380.0722.961129315111100
3.38-3.650.06326.251045414101100
3.65-40.05530.0495321300199.9
4-4.470.05232.1186101180199.8
4.47-5.160.05132.8474211015199.7
5.16-6.320.05628.646564880199.9
6.32-8.940.04931.854915671199.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.061 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 888 5.1 %RANDOM
Rwork0.2096 ---
all0.2124 32923 --
obs0.2124 32726 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.75 Å2 / Biso mean: 25.956 Å2 / Biso min: 7.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20 Å2
2--1.86 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 16 153 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191896
X-RAY DIFFRACTIONr_bond_other_d0.0010.021890
X-RAY DIFFRACTIONr_angle_refined_deg1.512.0022584
X-RAY DIFFRACTIONr_angle_other_deg0.80434351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48525.46964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.515334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.201158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_mcbond_it0.921.458998
X-RAY DIFFRACTIONr_mcbond_other0.9121.456997
X-RAY DIFFRACTIONr_mcangle_it1.5142.181248
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 62 -
Rwork0.205 1094 -
all-1156 -
obs--91.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.291-0.20740.35380.4814-0.4272.3648-0.00480.0911-0.1755-0.0441-0.0251-0.00440.19170.26310.02990.06770.0340.00670.0521-0.02820.060824.05083.933327.8898
21.5053-0.45721.16530.4649-0.03821.3120.02270.03720.0174-0.0348-0.00670.0434-0.03060.0672-0.0160.08490.00220.0160.067-0.00110.06566.683611.145212.989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 159
2X-RAY DIFFRACTION2A160 - 268

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