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

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Basic information

Entry
Database: PDB / ID: 4blu
TitleCrystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ
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 / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)67,98625
Polymers66,1782
Non-polymers1,80823
Water10,034557
1
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7109
Polymers33,0891
Non-polymers6218
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)34,27616
Polymers33,0891
Non-polymers1,18715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.870, 77.750, 82.500
Angle α, β, γ (deg.)90.00, 104.00, 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 3:52 OR RESSEQ 56: 280))
211(CHAIN B AND (RESSEQ 3:52 OR RESSEQ 56: 280))

NCS oper:
IDCodeMatrixVector
1given(-1, -0.0078, 0.0028), (-0.0046, 0.8088, 0.5881), (-0.0068, 0.588, -0.8088)50.4565, -17.7383, 55.1489
2given(-1, -0.0078, 0.0028), (-0.0046, 0.8088, 0.5881), (-0.0068, 0.588, -0.8088)50.4565, -17.7383, 55.1489

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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, 580 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 1.85→40 Å / Num. obs: 48904 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.025 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 19.89 / Stereochemistry target values: ML
Details: RESIDUES 53-55 IN CHAIN B ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.2064 2446 5 %
Rwork0.1663 --
obs0.1683 48903 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.64 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 115 557 5144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014797
X-RAY DIFFRACTIONf_angle_d1.226499
X-RAY DIFFRACTIONf_dihedral_angle_d14.4651849
X-RAY DIFFRACTIONf_chiral_restr0.08703
X-RAY DIFFRACTIONf_plane_restr0.006829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A275X-RAY DIFFRACTIONPOSITIONAL
12B275X-RAY DIFFRACTIONPOSITIONAL0.26
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88780.30991380.27982619X-RAY DIFFRACTION96
1.8878-1.92880.27311440.24882722X-RAY DIFFRACTION100
1.9288-1.97370.25131430.21152725X-RAY DIFFRACTION100
1.9737-2.02310.21021440.17382736X-RAY DIFFRACTION100
2.0231-2.07780.24721420.17572695X-RAY DIFFRACTION100
2.0778-2.13890.22781450.17542759X-RAY DIFFRACTION100
2.1389-2.20790.22691430.17272721X-RAY DIFFRACTION100
2.2079-2.28680.25971440.17492737X-RAY DIFFRACTION100
2.2868-2.37840.19951430.15632720X-RAY DIFFRACTION100
2.3784-2.48660.22651450.16512744X-RAY DIFFRACTION100
2.4866-2.61770.21341440.16292744X-RAY DIFFRACTION100
2.6177-2.78170.20981440.16382732X-RAY DIFFRACTION100
2.7817-2.99640.2351440.16832734X-RAY DIFFRACTION100
2.9964-3.29780.20091450.15732750X-RAY DIFFRACTION100
3.2978-3.77470.16761450.14462755X-RAY DIFFRACTION100
3.7747-4.75450.13691460.13342776X-RAY DIFFRACTION100
4.7545-40.0340.18811470.16012788X-RAY DIFFRACTION99

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