[English] 日本語
Yorodumi
- PDB-4auk: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4auk
TitleCrystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli
ComponentsRIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
KeywordsTRANSFERASE / YGDE
Function / homology
Function and homology information


23S rRNA (cytidine2498-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / cytoplasm
Similarity search - Function
THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase ...THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Ribosomal RNA large subunit methyltransferase M
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPunekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal Structure of Rlmm, the 2'O-Ribose Methyltransferase for C2498 of Escherichia Coli 23S Rrna.
Authors: Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
History
DepositionMay 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,67932
Polymers86,2492
Non-polymers2,43130
Water9,944552
1
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81421
Polymers43,1241
Non-polymers1,69020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,86511
Polymers43,1241
Non-polymers74110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.800, 132.800, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2589, 0.9659, 0.0092), (0.9659, -0.2588, -0.0098), (-0.0071, 0.0114, -0.9999)
Vector: 61.4002, -79.7765, 0.6797)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M / / 23S RRNA (CYTIDINE2498-2'-O)-METHYLTRANSFERASE / 23S RRNA 2'-O-RIBOSE METHYLTRANSFERASE RLMM


Mass: 43124.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEXP5-CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ADR6, 23S rRNA (cytidine2498-2'-O)-methyltransferase

-
Non-polymers , 8 types, 582 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsCATALYZES THE 2'-O-METHYLATION AT NUCLEOTIDE C2498 IN 23S RRNA OF ESCHERICHIA COLI

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.93 % / Description: NONE
Crystal growpH: 8.5
Details: 0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Dec 15, 2011 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→20.1 Å / Num. obs: 64264 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.72
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.57 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.42 / % possible all: 98.2

-
Processing

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

4atn


Resolution: 1.9→20.118 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 3212 5 %
Rwork0.1639 --
obs0.1661 64264 99.75 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.638 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.0297 Å20 Å20 Å2
2--0.0297 Å20 Å2
3----0.0594 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 157 552 6452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166096
X-RAY DIFFRACTIONf_angle_d1.5678221
X-RAY DIFFRACTIONf_dihedral_angle_d14.2832293
X-RAY DIFFRACTIONf_chiral_restr0.109860
X-RAY DIFFRACTIONf_plane_restr0.0071057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.92860.40511310.33072517X-RAY DIFFRACTION95
1.9286-1.95870.28391420.21472685X-RAY DIFFRACTION100
1.9587-1.99080.2591390.19132639X-RAY DIFFRACTION100
1.9908-2.02510.21791380.17292628X-RAY DIFFRACTION100
2.0251-2.06190.2251410.17232688X-RAY DIFFRACTION100
2.0619-2.10150.24071400.1742659X-RAY DIFFRACTION100
2.1015-2.14440.22171420.16692692X-RAY DIFFRACTION100
2.1444-2.19090.22331380.16092629X-RAY DIFFRACTION100
2.1909-2.24180.23921410.16252665X-RAY DIFFRACTION100
2.2418-2.29780.23371390.15792655X-RAY DIFFRACTION100
2.2978-2.35990.20551410.16652677X-RAY DIFFRACTION100
2.3599-2.42920.21561400.16722650X-RAY DIFFRACTION100
2.4292-2.50740.22761390.17362643X-RAY DIFFRACTION100
2.5074-2.59690.22241420.17112696X-RAY DIFFRACTION100
2.5969-2.70060.21621380.17412633X-RAY DIFFRACTION100
2.7006-2.82320.241400.17562650X-RAY DIFFRACTION100
2.8232-2.97160.20111410.17562690X-RAY DIFFRACTION100
2.9716-3.15720.21161410.16512672X-RAY DIFFRACTION100
3.1572-3.39980.17621400.15792665X-RAY DIFFRACTION100
3.3998-3.740.2111400.15152647X-RAY DIFFRACTION100
3.74-4.27670.17191390.13612640X-RAY DIFFRACTION100
4.2767-5.37110.14721400.12912670X-RAY DIFFRACTION100
5.3711-20.11930.16551400.15832662X-RAY DIFFRACTION100

+
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