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

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Basic information

Entry
Database: PDB / ID: 4blw
TitleCrystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylhomocysteine (AdoHcy) and Adenosine monophosphate (AMP)
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
ADENOSINE MONOPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 17, 2014Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_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

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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)68,92826
Polymers66,1782
Non-polymers2,75124
Water6,035335
1
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68216
Polymers33,0891
Non-polymers1,59315
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)34,24610
Polymers33,0891
Non-polymers1,1579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 77.060, 84.370
Angle α, β, γ (deg.)90.00, 99.50, 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 1:279))
211(CHAIN B AND (RESSEQ 1:279))

NCS oper: (Code: given
Matrix: (-1, -0.0035, 0.0062), (0.0007, 0.818, 0.5752), (-0.0071, 0.5752, -0.818)
Vector: 50.2745, -17.6654, 55.9049)

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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 BL21(DE3) (bacteria)
References: UniProt: P37634, 23S rRNA (adenine2030-N6)-methyltransferase

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Non-polymers , 7 types, 359 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.3 Å3/Da / Density % sol: 46 % / 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.3776
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.95→46 Å / Num. obs: 41777 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 23.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8

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Processing

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

4blu


Resolution: 1.95→45.951 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.85 / Stereochemistry target values: ML
Details: RESIDUE 280 IN CHAIN B IS DISORDERED AND WAS NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.1991 2088 5 %
Rwork0.167 --
obs0.1686 41772 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 179 335 5017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014842
X-RAY DIFFRACTIONf_angle_d1.3156563
X-RAY DIFFRACTIONf_dihedral_angle_d14.4881856
X-RAY DIFFRACTIONf_chiral_restr0.074711
X-RAY DIFFRACTIONf_plane_restr0.008826
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A279X-RAY DIFFRACTIONPOSITIONAL
12B279X-RAY DIFFRACTIONPOSITIONAL0.184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99540.25151360.22952582X-RAY DIFFRACTION96
1.9954-2.04530.24551400.20722662X-RAY DIFFRACTION97
2.0453-2.10060.23021370.19772610X-RAY DIFFRACTION97
2.1006-2.16240.24981370.1912623X-RAY DIFFRACTION97
2.1624-2.23220.25361370.19242601X-RAY DIFFRACTION95
2.2322-2.3120.22921400.18752659X-RAY DIFFRACTION98
2.312-2.40450.24591380.17382628X-RAY DIFFRACTION98
2.4045-2.51390.20211400.17472657X-RAY DIFFRACTION97
2.5139-2.64650.21741360.16872582X-RAY DIFFRACTION95
2.6465-2.81230.19731420.16842686X-RAY DIFFRACTION98
2.8123-3.02940.1961390.1652659X-RAY DIFFRACTION98
3.0294-3.33410.22071380.16922619X-RAY DIFFRACTION96
3.3341-3.81640.151430.14832703X-RAY DIFFRACTION99
3.8164-4.80740.14731400.1382666X-RAY DIFFRACTION97
4.8074-45.96380.20691450.16222747X-RAY DIFFRACTION98

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