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- PDB-6qe5: Structure of E.coli RlmJ in complex with the natural cofactor pro... -

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Basic information

Entry
Database: PDB / ID: 6qe5
TitleStructure of E.coli RlmJ in complex with the natural cofactor product S-adenosyl-homocysteine (SAH)
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
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesEscherichia coli PCN033 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 4, 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

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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)69,0914
Polymers68,3222
Non-polymers7692
Water5,098283
1
A: Ribosomal RNA large subunit methyltransferase J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5452
Polymers34,1611
Non-polymers3841
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)34,5452
Polymers34,1611
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.218, 46.224, 71.361
Angle α, β, γ (deg.)79.58, 77.59, 70.35
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 34161.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli PCN033 (bacteria) / 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M KSCN, 30% (w/v) polyethylene glycol methyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.61→43.23 Å / Num. obs: 67854 / % possible obs: 97.11 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07581 / Net I/σ(I): 9.89
Reflection shellResolution: 1.61→1.67 Å

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Processing

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

4blv


Resolution: 1.61→43.228 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 3422 5.05 %
Rwork0.1888 --
obs0.1904 67826 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→43.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 52 283 4697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064567
X-RAY DIFFRACTIONf_angle_d0.9356203
X-RAY DIFFRACTIONf_dihedral_angle_d9.0993843
X-RAY DIFFRACTIONf_chiral_restr0.055675
X-RAY DIFFRACTIONf_plane_restr0.005792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6330.32771320.25732602X-RAY DIFFRACTION96
1.633-1.65740.33761460.26012701X-RAY DIFFRACTION96
1.6574-1.68330.25521370.24732593X-RAY DIFFRACTION96
1.6833-1.71090.26671290.23412732X-RAY DIFFRACTION96
1.7109-1.74040.26791350.23242599X-RAY DIFFRACTION96
1.7404-1.7720.26571560.23332685X-RAY DIFFRACTION96
1.772-1.80610.27961350.21862648X-RAY DIFFRACTION96
1.8061-1.8430.26021580.20932711X-RAY DIFFRACTION97
1.843-1.88310.25341300.20152636X-RAY DIFFRACTION97
1.8831-1.92690.19661550.2062692X-RAY DIFFRACTION97
1.9269-1.9750.2351470.20412634X-RAY DIFFRACTION97
1.975-2.02840.24581200.1992691X-RAY DIFFRACTION97
2.0284-2.08810.24051560.20492691X-RAY DIFFRACTION97
2.0881-2.15550.26271430.19142659X-RAY DIFFRACTION97
2.1555-2.23260.20171580.18622655X-RAY DIFFRACTION97
2.2326-2.32190.21611370.18442749X-RAY DIFFRACTION98
2.3219-2.42760.19081420.18422706X-RAY DIFFRACTION98
2.4276-2.55560.24931550.19672672X-RAY DIFFRACTION98
2.5556-2.71570.24021660.19512701X-RAY DIFFRACTION98
2.7157-2.92530.24011200.19922722X-RAY DIFFRACTION98
2.9253-3.21960.21111440.19272713X-RAY DIFFRACTION98
3.2196-3.68530.22391370.17262737X-RAY DIFFRACTION99
3.6853-4.64220.1481450.14642757X-RAY DIFFRACTION99
4.6422-43.24310.1921390.15432718X-RAY DIFFRACTION99

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