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- PDB-3m4x: Structure of a ribosomal methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3m4x
TitleStructure of a ribosomal methyltransferase
ComponentsNOL1/NOP2/sun family protein
KeywordsTRANSFERASE / MTase domain / PUA domain / RRM motif
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / methylation / RNA binding
Similarity search - Function
rRNA small subunit methyltransferase F, RNA-binding PUA-like domain / RNA-binding PUA-like domain of methyltransferase RsmF / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 ...rRNA small subunit methyltransferase F, RNA-binding PUA-like domain / RNA-binding PUA-like domain of methyltransferase RsmF / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #60 / Ribosomal RNA small subunit methyltransferase F, first C-terminal domain / RsmF rRNA methyltransferase first C-terminal domain / Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 / Roll / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA/rRNA methyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsGalimand, M. / Schmitt, E. / Panvert, M. / Mechulam, Y. / Courvalin, P.
CitationJournal: To be Published
Title: Structure of an RNA methyltransferase
Authors: Galimand, M. / Schmitt, E. / Panvert, M. / Mechulam, Y. / Courvalin, P.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NOL1/NOP2/sun family protein


Theoretical massNumber of molelcules
Total (without water)51,7521
Polymers51,7521
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.556, 98.556, 106.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NOL1/NOP2/sun family protein / rRNA Methyltransferase / EFM methyltransferase


Mass: 51751.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: CIP 54-32 / Gene: EfmM / Plasmid: Pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q3Y1J9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN IS THE SAME AS DATABASE UNIPROTKB/TREMBL C9C5U0 (C9C5U0_ENTFC), BUT THE ...THE SEQUENCE OF THE PROTEIN IS THE SAME AS DATABASE UNIPROTKB/TREMBL C9C5U0 (C9C5U0_ENTFC), BUT THE STRAIN OF THE SOURCE ORGANISM IS DIFFERENT.

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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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% Peg 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.28→36.099 Å / Num. all: 24457 / Num. obs: 24384 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.94 % / Biso Wilson estimate: 41.36 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 14.05
Reflection shellResolution: 2.28→2.35 Å / Redundancy: 6.52 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.18 / Rsym value: 0.397 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2FRX

2frx


Resolution: 2.28→33.896 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.819 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1235 5.07 %
Rwork0.1965 --
obs0.1993 24382 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.683 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 250.4 Å2 / Biso mean: 47.511 Å2 / Biso min: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1--7.36 Å2-0 Å20 Å2
2---7.36 Å20 Å2
3---14.721 Å2
Refinement stepCycle: LAST / Resolution: 2.28→33.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 83 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073575
X-RAY DIFFRACTIONf_angle_d1.1174836
X-RAY DIFFRACTIONf_dihedral_angle_d18.1241313
X-RAY DIFFRACTIONf_chiral_restr0.082515
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.37130.24651270.19372541X-RAY DIFFRACTION100
2.3713-2.47920.27751470.19522498X-RAY DIFFRACTION100
2.4792-2.60980.25351320.20982537X-RAY DIFFRACTION100
2.6098-2.77330.26141580.2082519X-RAY DIFFRACTION100
2.7733-2.98730.29521390.21032557X-RAY DIFFRACTION100
2.9873-3.28770.29421320.21232572X-RAY DIFFRACTION100
3.2877-3.76290.25351130.19442590X-RAY DIFFRACTION100
3.7629-4.73880.21441480.16382615X-RAY DIFFRACTION100
4.7388-33.90010.22041390.18092718X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.6265 Å / Origin y: 16.8107 Å / Origin z: 23.372 Å
111213212223313233
T0.2476 Å20.0244 Å20.0763 Å2-0.2394 Å2-0.0057 Å2--0.1767 Å2
L0.7235 °2-0.5212 °2-0.2026 °2-1.7159 °2-0.2412 °2--0.3432 °2
S-0.0576 Å °-0.148 Å °-0.0374 Å °0.203 Å °0.1979 Å °0.1958 Å °-0.0534 Å °0.037 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 455
2X-RAY DIFFRACTION1allA457 - 539

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