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- PDB-6qdx: Structure of E.coli RlmJ in complex with a bisubstrate analogue (BA4) -

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Basic information

Entry
Database: PDB / ID: 6qdx
TitleStructure of E.coli RlmJ in complex with a bisubstrate analogue (BA4)
ComponentsRibosomal RNA large subunit methyltransferase J
KeywordsTRANSFERASE / RNA MTases / methyltransferase / m6A / transition state analogue / inhibitor / RNA binding / TrmK / RlmJ / m1A / structure.
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
Chem-HY8 / Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
CitationJournal: Rna Biol. / Year: 2019
Title: Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.
Authors: Oerum, S. / Catala, M. / Atdjian, C. / Brachet, F. / Ponchon, L. / Barraud, P. / Iannazzo, L. / Droogmans, L. / Braud, E. / Etheve-Quelquejeu, M. / Tisne, C.
History
DepositionJan 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Ribosomal RNA large subunit methyltransferase J
D: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7868
Polymers129,0884
Non-polymers2,6994
Water12,809711
1
A: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9472
Polymers32,2721
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9472
Polymers32,2721
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9472
Polymers32,2721
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9472
Polymers32,2721
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.420, 170.730, 66.590
Angle α, β, γ (deg.)90.00, 118.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosomal RNA large subunit methyltransferase J / 23STSA4 / rRNA (adenine(2030)-N6)-methyltransferase / 23S rRNA m6A2030 methyltransferase


Mass: 32271.955 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yhiR, rlmJ, PPECC33_03818 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0G3KF30, UniProt: P37634*PLUS, 23S rRNA (adenine2030-N6)-methyltransferase
#2: Chemical
ChemComp-HY8 / (2~{S})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{S},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid


Mass: 674.666 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H38N12O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MMT pH 6.0, 25% (w/v) PEG1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98007 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98007 Å / Relative weight: 1
ReflectionResolution: 2.1→48.323 Å / Num. obs: 75173 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.2072 / Net I/σ(I): 5.63
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.7769

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLV

4blv


Resolution: 2.1→48.323 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 3751 4.99 %
Rwork0.2182 --
obs0.221 75113 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 175 711 9585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089107
X-RAY DIFFRACTIONf_angle_d1.05112376
X-RAY DIFFRACTIONf_dihedral_angle_d11.1775401
X-RAY DIFFRACTIONf_chiral_restr0.0641354
X-RAY DIFFRACTIONf_plane_restr0.0061568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12660.35281440.28862577X-RAY DIFFRACTION97
2.1266-2.15460.33961230.2792614X-RAY DIFFRACTION97
2.1546-2.18410.30831220.26642629X-RAY DIFFRACTION99
2.1841-2.21530.3521460.25622644X-RAY DIFFRACTION98
2.2153-2.24840.30351070.25252619X-RAY DIFFRACTION99
2.2484-2.28350.31441600.25022632X-RAY DIFFRACTION99
2.2835-2.32090.29991110.23732600X-RAY DIFFRACTION98
2.3209-2.36090.31671180.22732684X-RAY DIFFRACTION99
2.3609-2.40390.26351290.2322622X-RAY DIFFRACTION98
2.4039-2.45010.29061330.2232656X-RAY DIFFRACTION99
2.4501-2.50010.31351410.22632599X-RAY DIFFRACTION99
2.5001-2.55450.29771510.23552668X-RAY DIFFRACTION99
2.5545-2.61390.31431360.23632618X-RAY DIFFRACTION99
2.6139-2.67930.32091460.23422610X-RAY DIFFRACTION99
2.6793-2.75170.32881230.22752666X-RAY DIFFRACTION100
2.7517-2.83270.30431520.22812630X-RAY DIFFRACTION99
2.8327-2.92410.31941460.21522661X-RAY DIFFRACTION99
2.9241-3.02860.26131510.21642630X-RAY DIFFRACTION99
3.0286-3.14980.28291240.20982682X-RAY DIFFRACTION100
3.1498-3.29310.28731520.22152639X-RAY DIFFRACTION100
3.2931-3.46670.29411290.21332680X-RAY DIFFRACTION100
3.4667-3.68380.25121240.19872680X-RAY DIFFRACTION99
3.6838-3.96810.23661420.19822656X-RAY DIFFRACTION100
3.9681-4.36720.23241450.19262666X-RAY DIFFRACTION100
4.3672-4.99860.2241400.18342666X-RAY DIFFRACTION100
4.9986-6.29550.23961800.22042654X-RAY DIFFRACTION100
6.2955-48.33620.24671760.22822680X-RAY DIFFRACTION100

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