[English] 日本語
Yorodumi
- PDB-1ej0: FTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE, M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ej0
TitleFTSJ RNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYLMETHIONINE, MERCURY DERIVATIVE
ComponentsFTSJ
KeywordsTRANSFERASE / ftsj / methyltransferase / adomet / adenosyl methionine / heat shock proteins / 23S RIBOSOMAL RNA
Function / homology
Function and homology information


23S rRNA (uridine2552-2'-O)-methyltransferase / rRNA (uridine-2'-O-)-methyltransferase activity / RNA methylation / rRNA processing / ribosomal large subunit assembly / cytoplasm / cytosol
Similarity search - Function
Ribosomal RNA methyltransferase E, gammaproteobacteria / : / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase E / Ribosomal RNA large subunit methyltransferase E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBugl, H. / Fauman, E.B. / Staker, B.L. / Zheng, F. / Kushner, S.R. / Saper, M.A. / Bardwell, J.C.A. / Jakob, U.
Citation
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The FtsJ/RrmJ heat shock protein of escherichia coli is a 23 S ribosomal RNA methyltransferase.
Authors: Caldas, T. / Binet, E. / Bouloc, P. / Costa, A. / Desgres, J. / Richarme, G.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FTSJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7374
Polymers19,9371
Non-polymers8003
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.579, 65.872, 72.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

-
Components

#1: Protein FTSJ / FTSJ METHYLTRANSFERASE


Mass: 19937.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P28692, UniProt: P0C0R7*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.65
Details: 1mM Adomet, 33% PEG 4000, 0.19 ammonium acetate, 0.1 M sodium citrate pH 5.65, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlFtsJ1drop
21 mMAdoMet1drop
333 %PEG40001reservoir
40.19 Mammonium acetate1reservoir
50.1 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 54471 / Num. obs: 51445 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.38 / % possible all: 62

-
Processing

Software
NameClassification
CNSrefinement
bioteXdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIZ

1eiz


Resolution: 1.5→17.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 87999367.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction. Used anomalous data.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2608 5.1 %RANDOM
Rwork0.198 ---
obs0.198 51445 94.5 %-
all-54471 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.77 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2--0.43 Å20 Å2
3----1.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→17.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 29 182 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.842
X-RAY DIFFRACTIONc_scangle_it3.572.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.367 242 4.9 %
Rwork0.345 4695 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5MYSAM.PARAMMYSAM.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.45
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.345

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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