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- PDB-4j3c: Crystal structure of 16S ribosomal RNA methyltransferase RsmE -

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Basic information

Entry
Database: PDB / ID: 4j3c
TitleCrystal structure of 16S ribosomal RNA methyltransferase RsmE
ComponentsRibosomal RNA small subunit methyltransferase E
KeywordsTRANSFERASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / Three Layer / Two Domains / Methylation / rRNA Processing / S-adenosyl-L-methionine
Function / homology
Function and homology information


16S rRNA (uracil1498-N3)-methyltransferase / methyltransferase activity / rRNA processing / methylation / cytoplasm
Similarity search - Function
Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel ...Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of 16S ribosomal RNA methyltransferase RsmE
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release

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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 E
B: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)60,2032
Polymers60,2032
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-10 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.085, 152.082, 38.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase E


Mass: 30101.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00771, SMc00826 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q92RS8, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG3350, 0.1M HEPES, 0.2M L-Proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9733 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013 / Details: mirrors
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9733 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 39489 / Num. obs: 39489 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.716 / Num. unique all: 3175 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.116 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 1969 5 %RANDOM
Rwork0.24639 ---
all0.325 39281 --
obs0.24838 37312 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---2.59 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 60 3612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223608
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9824891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19623.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6111539
X-RAY DIFFRACTIONr_chiral_restr0.0990.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212730
X-RAY DIFFRACTIONr_mcbond_it0.7661.52313
X-RAY DIFFRACTIONr_mcangle_it1.423688
X-RAY DIFFRACTIONr_scbond_it2.37431295
X-RAY DIFFRACTIONr_scangle_it3.8464.51203
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 141 -
Rwork0.321 2673 -
obs-2814 97.51 %
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)
12.7917-1.8392-0.60243.9230.57951.0955-0.05470.2745-0.0461-0.0616-0.0862-0.19570.0609-0.08730.14090.1671-0.0234-0.00990.15850.00150.048960.131510.470123.6531
20.33810.6593-0.38112.9804-0.48230.7405-0.11140.0968-0.0192-0.05710.0548-0.7368-0.0366-0.00380.05660.2256-0.0359-0.13150.22280.07230.549482.554423.232925.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 245
2X-RAY DIFFRACTION2B7 - 245

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