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- PDB-4e8b: Crystal structure of 16S rRNA Methyltransferase RsmE from E.coli -

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Basic information

Entry
Database: PDB / ID: 4e8b
TitleCrystal structure of 16S rRNA Methyltransferase RsmE from E.coli
ComponentsRibosomal RNA small subunit methyltransferase E
KeywordsTRANSFERASE / 16S rRNA Methyltransferase
Function / homology
Function and homology information


rRNA (uridine-N3-)-methyltransferase activity / 16S rRNA (uracil1498-N3)-methyltransferase / rRNA base 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m(3)U1498) from crystal and solution structures
Authors: Zhang, H. / Wan, H. / Gao, Z.Q. / Wei, Y. / Wang, W.J. / Liu, G.F. / Shtykova, E.V. / Xu, J.H. / Dong, Y.H.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)28,0841
Polymers28,0841
Non-polymers00
Water1,42379
1
A: Ribosomal RNA small subunit methyltransferase E

A: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)56,1682
Polymers56,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
2
A: Ribosomal RNA small subunit methyltransferase E

A: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)56,1682
Polymers56,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2840 Å2
ΔGint-8 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.479, 43.681, 74.883
Angle α, β, γ (deg.)90.00, 127.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase E / 16S rRNA Methyltransferase RsmE


Mass: 28084.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: rsmE / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AGL7, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M KSCN, 30%(w/v) PEG MME 2000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. all: 11818 / Num. obs: 11818 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 33.46 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.55
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.15 / Num. unique all: 596 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHY

1vhy


Resolution: 2.249→47.709 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.53 / σ(F): 0 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 561 4.75 %RANDOM
Rwork0.2071 ---
all0.2094 11818 --
obs0.2094 11817 99.79 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.604 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 97.54 Å2 / Biso mean: 42.9079 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.4509 Å20 Å22.3185 Å2
2---0.4127 Å2-0 Å2
3----0.0382 Å2
Refinement stepCycle: LAST / Resolution: 2.249→47.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 0 79 1958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011919
X-RAY DIFFRACTIONf_angle_d1.2462598
X-RAY DIFFRACTIONf_chiral_restr0.079299
X-RAY DIFFRACTIONf_plane_restr0.006341
X-RAY DIFFRACTIONf_dihedral_angle_d17.977736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2492-2.47560.33881320.245427872919
2.4756-2.83380.33221330.24327862919
2.8338-3.57010.27321340.221328242958
3.5701-47.72010.20831620.178528593021

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