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- PDB-2frx: Crystal structure of YebU, a m5C RNA methyltransferase from E.coli -

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Basic information

Entry
Database: PDB / ID: 2frx
TitleCrystal structure of YebU, a m5C RNA methyltransferase from E.coli
ComponentsHypothetical protein yebU
KeywordsTRANSFERASE / Rossmann-type S-adenosylmethionine-dependent methyltransferase domain / C-terminal PUA (pseudouridine synthases and archaeosine-specific transglycosylases) domain
Function / homology
Function and homology information


16S rRNA (cytosine1407-C5)-methyltransferase / rRNA (cytosine-C5-)-methyltransferase activity / RNA methylation / rRNA base methylation / RNA binding / cytoplasm
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #720 / rRNA small subunit methyltransferase F / rRNA small subunit methyltransferase F, RNA-binding PUA-like domain / RNA-binding PUA-like domain of methyltransferase RsmF / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type ...Nuclear Transport Factor 2; Chain: A, - #720 / rRNA small subunit methyltransferase F / rRNA small subunit methyltransferase F, RNA-binding PUA-like domain / RNA-binding PUA-like domain of methyltransferase RsmF / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Nuclear Transport Factor 2; Chain: A, / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsErlandsen, H. / Nordlund, P. / Hallberg, B.M. / Johnson, K.A. / Ericsson, U.B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain
Authors: Hallberg, B.M. / Ericsson, U.B. / Johnson, K.A. / Andersen, N.M. / Douthwaite, S. / Nordlund, P. / Beuscher IV, A.E. / Erlandsen, H.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yebU
B: Hypothetical protein yebU
C: Hypothetical protein yebU
D: Hypothetical protein yebU


Theoretical massNumber of molelcules
Total (without water)214,6344
Polymers214,6344
Non-polymers00
Water00
1
A: Hypothetical protein yebU


Theoretical massNumber of molelcules
Total (without water)53,6581
Polymers53,6581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yebU


Theoretical massNumber of molelcules
Total (without water)53,6581
Polymers53,6581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein yebU


Theoretical massNumber of molelcules
Total (without water)53,6581
Polymers53,6581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein yebU


Theoretical massNumber of molelcules
Total (without water)53,6581
Polymers53,6581
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.706, 87.126, 95.048
Angle α, β, γ (deg.)88.33, 76.79, 90.19
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PHE / End label comp-ID: LEU / Refine code: 3 / Auth seq-ID: 8 - 474 / Label seq-ID: 8 - 474

Dom-IDAuth asym-IDLabel asym-ID
1CC
2AA
3BB
4DD

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Components

#1: Protein
Hypothetical protein yebU / RNA m5C methyltransferase


Mass: 53658.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YebU / Plasmid: PT73.3HisGW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76273

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15%(w/v) PEG 8000, 50mM mono-potassium dihydrogen phosphate, 10mM BaCl2 or 15% PEG 5000 MME, sodium acetate pH 4.6, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.962 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 19, 2003
Details: Mirror followed by asymmetrically cut Si-111 monochromator
RadiationMonochromator: Mirror followed by asymmetrically cut Si-111 monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 46876 / Num. obs: 45870 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.22 % / Rsym value: 0.103 / Net I/σ(I): 9.13
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 4493 / Rsym value: 0.551 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.03 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 49.191 / SU ML: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2314 5.1 %RANDOM
Rwork0.231 ---
all0.234 46791 --
obs0.234 45743 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.522 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.01 Å20.04 Å2
2--0.03 Å2-0.05 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14266 0 0 0 14266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02214636
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.93619901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61351806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80723.709693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.484152319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.28115111
X-RAY DIFFRACTIONr_chiral_restr0.1240.22150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211375
X-RAY DIFFRACTIONr_nbd_refined0.2640.27353
X-RAY DIFFRACTIONr_nbtor_refined0.3260.29870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2426
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.213
X-RAY DIFFRACTIONr_mcbond_it0.5321.59264
X-RAY DIFFRACTIONr_mcangle_it0.798214587
X-RAY DIFFRACTIONr_scbond_it1.66136107
X-RAY DIFFRACTIONr_scangle_it2.5244.55314
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C1812TIGHT POSITIONAL0.060.05
2A1812TIGHT POSITIONAL0.060.05
3B1812TIGHT POSITIONAL0.060.05
4D1812TIGHT POSITIONAL0.060.05
1C1739LOOSE POSITIONAL0.825
2A1739LOOSE POSITIONAL0.785
3B1739LOOSE POSITIONAL0.765
4D1739LOOSE POSITIONAL0.745
1C1812TIGHT THERMAL0.10.5
2A1812TIGHT THERMAL0.090.5
3B1812TIGHT THERMAL0.110.5
4D1812TIGHT THERMAL0.090.5
1C1739LOOSE THERMAL1.5910
2A1739LOOSE THERMAL1.6510
3B1739LOOSE THERMAL1.8510
4D1739LOOSE THERMAL1.4910
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 159 -
Rwork0.298 3188 -
obs-3347 97.52 %
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)
12.9944-1.8184-1.1412.67870.51262.11260.27430.35780.0257-0.706-0.3099-0.41230.2088-0.04690.03550.0680.26450.057-0.1847-0.0215-0.14331.7278.68376.622
23.84420.5456-0.65222.4195-0.84332.04090.010.4839-0.0915-0.3075-0.0677-0.10970.42150.12290.0576-0.37150.109-0.0283-0.2458-0.0694-0.32735.30754.60667.011
34.3852-0.6592-0.79892.52120.79252.17030.0763-0.5283-0.25690.4517-0.17260.30570.4979-0.15360.0963-0.2472-0.12910.0082-0.22350.0494-0.2559-10.0357.89825.644
42.87951.7689-1.32053.0957-0.55482.58280.2214-0.26890.16140.8064-0.23310.51280.2775-0.01910.01170.1892-0.23960.1058-0.1886-0.0169-0.174531.20549.26715.974
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 8 - 474 / Label seq-ID: 8 - 474

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD

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