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- PDB-4atn: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -

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Basic information

Entry
Database: PDB / ID: 4atn
TitleCrystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli
ComponentsRIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
KeywordsTRANSFERASE
Function / homology
Function and homology information


23S rRNA (cytidine2498-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / rRNA processing / cytoplasm
Similarity search - Function
THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase ...THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase M
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPunekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal Structure of Rlmm, the 2'O-Ribose Methyltransferase for C2498 of Escherichia Coli 23S Rrna.
Authors: Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
History
DepositionMay 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,24131
Polymers43,0921
Non-polymers2,14830
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.090, 92.090, 83.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M / 23S RRNA (CYTIDINE2498-2'-O)-METHYLTRANSFERASE / 23S RRNA 2'-O-RIBOSE METHYLTRANSFERASE RLMM


Mass: 43092.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEXP5-CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ADR6, 23S rRNA (cytidine2498-2'-O)-methyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE 2'-O-METHYLATION AT NUCLEOTIDE C2498 IN 23S RRNA OF ESCHERICHIA COLI
Has protein modificationY
Sequence detailsHAS 6XHIS-TAG AT THE C-TERMINAL END

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.5
Details: 0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350, 3.0% DEXTRAN SULFATE SODIUM SALT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 7, 2012
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING OPTICS MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.95→28.77 Å / Num. obs: 30022 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 33.02 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.5 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL OBTAINED FROM K2PTCL4 DERIVATIVE CRYSTAL DATA

Resolution: 1.95→28.769 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 1502 5 %
Rwork0.1688 --
obs0.1707 30022 99.77 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.848 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.5099 Å20 Å20 Å2
2---1.5099 Å20 Å2
3---3.0198 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2880 0 134 195 3209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083103
X-RAY DIFFRACTIONf_angle_d1.0724168
X-RAY DIFFRACTIONf_dihedral_angle_d15.0011156
X-RAY DIFFRACTIONf_chiral_restr0.074432
X-RAY DIFFRACTIONf_plane_restr0.005530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01290.2761330.23512524X-RAY DIFFRACTION99
2.0129-2.08490.28461350.20222560X-RAY DIFFRACTION100
2.0849-2.16830.24421360.19522588X-RAY DIFFRACTION100
2.1683-2.2670.27521330.20222529X-RAY DIFFRACTION99
2.267-2.38640.25861360.18452583X-RAY DIFFRACTION100
2.3864-2.53590.22371360.16822585X-RAY DIFFRACTION100
2.5359-2.73150.23081360.16762573X-RAY DIFFRACTION100
2.7315-3.00610.22591370.16872599X-RAY DIFFRACTION100
3.0061-3.44050.2041370.15492615X-RAY DIFFRACTION100
3.4405-4.33230.15461390.1472629X-RAY DIFFRACTION100
4.3323-28.77170.18861440.17192735X-RAY DIFFRACTION100

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