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- PDB-4blv: Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyl... -

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Basic information

Entry
Database: PDB / ID: 4blv
TitleCrystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylmethionine (AdoMet)
ComponentsRIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
KeywordsTRANSFERASE / N6-METHYLADENINE / ROSSMANN-LIKE FOLD / SUBDOMAIN INSERTION
Function / homology
Function and homology information


23S rRNA (adenine2030-N6)-methyltransferase / 23S rRNA (adenine(2030)-N(6))-methyltransferase activity / rRNA (adenine-N6-)-methyltransferase activity / carbon utilization / rRNA base methylation / RNA binding / cytosol
Similarity search - Function
Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase D, RlmJ / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPunekar, A.S. / Liljeruhm, J. / Shepherd, T.R. / Forster, A.C. / Selmer, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj.
Authors: Punekar, A.S. / Liljeruhm, J. / Shepherd, T.R. / Forster, A.C. / Selmer, M.
History
DepositionMay 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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_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_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: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,14736
Polymers66,1782
Non-polymers2,96934
Water7,909439
1
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68519
Polymers33,0891
Non-polymers1,59618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,46217
Polymers33,0891
Non-polymers1,37416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.680, 77.570, 82.700
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 7:50 OR RESSEQ 59: 132 OR RESSEQ 134:165 OR RESSEQ 171:280))
211(CHAIN B AND (RESSEQ 7:50 OR RESSEQ 59: 132 OR RESSEQ 134:165 OR RESSEQ 171:280))

NCS oper:
IDCodeMatrixVector
1given(-0.9999, -0.0115, -0.0022), (-0.0106, 0.8122, 0.5832), (-0.0049, 0.5832, -0.8123)50.3529, -17.3796, 55.3789
2given(-0.9999, -0.0115, -0.0022), (-0.0106, 0.8122, 0.5832), (-0.0049, 0.5832, -0.8123)50.3529, -17.3796, 55.3789
3given(-0.9999, -0.0115, -0.0022), (-0.0106, 0.8122, 0.5832), (-0.0049, 0.5832, -0.8123)50.3529, -17.3796, 55.3789
4given(-0.9999, -0.0115, -0.0022), (-0.0106, 0.8122, 0.5832), (-0.0049, 0.5832, -0.8123)50.3529, -17.3796, 55.3789

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J /


Mass: 33088.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SPECIFICALLY MONOMETHYLATES THE ADENINE IN POSITION 2030 OF 23S RRNA
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: P37634, 23S rRNA (adenine2030-N6)-methyltransferase

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Non-polymers , 6 types, 473 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M SODIUM SULFATE DECAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 6, 2012 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→45.4 Å / Num. obs: 38776 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 18.54 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BLU

4blu


Resolution: 2→45.39 Å / SU ML: 0.25 / σ(F): 2.01 / Phase error: 20.61 / Stereochemistry target values: ML
Details: RESIDUES 53-55 IN CHAIN B ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.2127 2009 5.2 %
Rwork0.1696 --
obs0.1719 38775 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.62 Å2
Refinement stepCycle: LAST / Resolution: 2→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 192 439 5111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174858
X-RAY DIFFRACTIONf_angle_d1.5026560
X-RAY DIFFRACTIONf_dihedral_angle_d15.5871876
X-RAY DIFFRACTIONf_chiral_restr0.091709
X-RAY DIFFRACTIONf_plane_restr0.008831
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A260X-RAY DIFFRACTIONPOSITIONAL
12B260X-RAY DIFFRACTIONPOSITIONAL0.416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30191390.26912586X-RAY DIFFRACTION100
2.05-2.10550.30681560.24342618X-RAY DIFFRACTION100
2.1055-2.16740.29741340.21592623X-RAY DIFFRACTION100
2.1674-2.23740.26771440.1912623X-RAY DIFFRACTION100
2.2374-2.31730.23671390.19272614X-RAY DIFFRACTION100
2.3173-2.41010.21521390.17542595X-RAY DIFFRACTION100
2.4101-2.51980.24561410.16882639X-RAY DIFFRACTION100
2.5198-2.65260.21931390.16432623X-RAY DIFFRACTION100
2.6526-2.81880.23561440.17392631X-RAY DIFFRACTION100
2.8188-3.03640.22191380.16552638X-RAY DIFFRACTION100
3.0364-3.34190.20841440.15712630X-RAY DIFFRACTION100
3.3419-3.82530.1581380.14372634X-RAY DIFFRACTION100
3.8253-4.81860.15281460.13112645X-RAY DIFFRACTION100
4.8186-45.40190.19341680.16592667X-RAY DIFFRACTION99

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