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- PDB-1eiz: FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE -

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Basic information

Entry
Database: PDB / ID: 1eiz
TitleFTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE
ComponentsFTSJ
KeywordsTRANSFERASE / ftsj / methyltransferase / adomet / adenosyl methionine / heat shock proteinS / 23S RIBOSOMAL RNA
Function / homology
Function and homology information


23S rRNA (uridine2552-2'-O)-methyltransferase / rRNA (uridine-2'-O-)-methyltransferase activity / RNA methylation / rRNA processing / ribosomal large subunit assembly / cytoplasm / cytosol
Similarity search - Function
Ribosomal RNA methyltransferase E, gammaproteobacteria / : / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA large subunit methyltransferase E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsBugl, H. / Fauman, E.B. / Staker, B.L. / Zheng, F. / Kushner, S.R. / Saper, M.A. / Bardwell, J.C.A. / Jakob, U.
Citation
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The FtsJ/RrmJ heat shock protein of escherichia coli is a 23 S ribosomal RNA methyltransferase.
Authors: Caldas, T. / Binet, E. / Bouloc, P. / Costa, A. / Desgres, J. / Richarme, G.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FTSJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3362
Polymers19,9371
Non-polymers3981
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.457, 65.867, 72.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological assembly is a monomer in solution

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Components

#1: Protein FTSJ / FTSJ METHYLTRANSFERASE


Mass: 19937.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P28692, UniProt: P0C0R7*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.65
Details: 1mM AdoMet, 33% PEG 4000, 0.19 M ammonium acetate, 0.1 M sodium citrate pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlFtsJ1drop
21 mMAdoMet1drop
333 %PEG40001reservoir
40.19 Mammonium acetate1reservoir
50.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 29034 / Num. obs: 24364 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4 % / Rmerge(I) obs: 0.371 / Num. unique all: 1195 / % possible all: 62.1

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
bioteXdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→18.22 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1007 5.4 %RANDOM
Rwork0.19 ---
all-19959 --
obs-18697 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4512 Å2 / ksol: 0.394983 e/Å3
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20 Å2
2--2.77 Å20 Å2
3----5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 27 183 1599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0128
X-RAY DIFFRACTIONc_angle_deg1.697
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.389 106 5.9 %
Rwork0.369 1676 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5mysam.parmysam.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor obs: 0.191 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.389 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.369

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