[English] 日本語
Yorodumi
- PDB-4blw: Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyl... -

+
Open data


ID or keywords:

Loading...

-
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 D, RlmJ / Ribosomal RNA large subunit methyltransferase J / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
γ
α
β
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)

-
Components

-
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

-
Non-polymers , 7 types, 359 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / 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 / 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 / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

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

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more