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- PDB-3uzu: The structure of the Ribosomal RNA small subunit methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 3uzu
TitleThe structure of the Ribosomal RNA small subunit methyltransferase A from Burkholderia pseudomallei
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / RNA / SSGCID / Seattle Structural Genomics Center for Infectious Disease / methyltransferase A
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, 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 ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / 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 / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: The structure of the Ribosomal RNA small subunit methyltransferase A from Burkholderia pseudomallei
Authors: Clifton, M.C. / Abendroth, J. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,7073
Polymers30,5831
Non-polymers1242
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.190, 49.340, 61.160
Angle α, β, γ (deg.)90.000, 95.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-293-

HOH

21A-530-

HOH

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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: 30583.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: rsmA, ksgA, BURPS1710b_0874 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JVW6, UniProt: Q63X76*PLUS, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 150mM DL Malic Acid. Cryoprotectant 20% ethylene glycol. 47.14 mg/ml BupsA.01122.a.A1 PS01140, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→43.343 Å / Num. obs: 27262 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.266 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.4343.137563200099.9
1.8-1.840.3623.7274861975100
1.84-1.90.3324.327280191399.7
1.9-1.960.3035.576555178796.8
1.96-2.020.2196.846845179499.9
2.02-2.090.1888.716456174099.4
2.09-2.170.1549.776458169099.8
2.17-2.260.13711.455881159997.9
2.26-2.360.12612.715605153197.7
2.36-2.470.114.5856571480100
2.47-2.610.09215.795215140399.4
2.61-2.770.07518.365024131799.8
2.77-2.960.06320.154776126699.8
2.96-3.20.05922.454501118499.7
3.2-3.50.04826.773947108999.4
3.5-3.910.04129.55342296299.2
3.91-4.520.03531.62301187299
4.52-5.530.03132.59271574799.9
5.53-7.830.03131.44216957799.7
7.830.02236.74121133699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.35 Å
Translation2.5 Å45.35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QYR

1qyr


Resolution: 1.75→43.343 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2023 / WRfactor Rwork: 0.1656 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8667 / SU B: 4.182 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1188 / SU Rfree: 0.1151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1371 5 %RANDOM
Rwork0.1804 ---
obs0.1823 25892 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: 40.95 Å2 / Biso mean: 15.3075 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.04 Å2
2---0.05 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 8 278 2269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192048
X-RAY DIFFRACTIONr_bond_other_d0.0010.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9832788
X-RAY DIFFRACTIONr_angle_other_deg0.96133388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55722.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61915314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02426
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 88 -
Rwork0.236 1845 -
all-1933 -
obs--99.74 %
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)
11.02770.25390.05590.8041-0.06571.0333-0.0214-0.0806-0.07580.04350.0063-0.05350.07210.02940.0150.03410.0094-0.00150.03310.00590.02812.14613.656814.7219
20.87661.3085-0.77262.4903-0.74341.17930.0101-0.1598-0.20120.1296-0.1624-0.41270.04790.2260.15230.0449-0.0109-0.03150.0720.02330.09116.074522.216918.0176
31.0174-0.32020.10751.006-0.21330.4690.0015-0.0097-0.01980.07590.00610.0689-0.0264-0.0416-0.00760.0356-0.0015-0.00030.0306-0.00030.038621.522441.37955.286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 149
2X-RAY DIFFRACTION2A150 - 202
3X-RAY DIFFRACTION3A203 - 275

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