[English] 日本語
Yorodumi
- PDB-6aie: Crystal structure of a new form of RsmD-like RNA methyl transfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aie
TitleCrystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution
ComponentsPutative methyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


16S rRNA (guanine(966)-N(2))-methyltransferase activity / 16S rRNA (guanine966-N2)-methyltransferase / host cell nucleolus / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / nucleic acid binding / host cell cytoplasm / extracellular region
Similarity search - Function
Conserved hypothetical protein 95 / RNA methyltransferase, RsmD / 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
Methyltransferase / RNA/DNA methyltransferase Rv2966c
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsVenkataraman, S. / Dhankar, A. / Sinha, K.M. / Manivasakan, P. / Iqbal, N. / Singh, T.P. / Prasad, B.V.L.S.
CitationJournal: To Be Published
Title: Crystal structure of a new form of RsmD-like RNA methyl transferase from Mycobacterium tuberculosis determined at 1.74 A resolution
Authors: Venkataraman, S. / Dhankar, A. / Sinha, K.M. / Bandopadhyay, K. / Iqbal, N. / Singh, T.P. / Prasad, V.L.S.B.
History
DepositionAug 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative methyltransferase
B: Putative methyltransferase
C: Putative methyltransferase


Theoretical massNumber of molelcules
Total (without water)59,7443
Polymers59,7443
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.782, 55.300, 100.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative methyltransferase / RsmD-like RNA methyltransferase


Mass: 19914.572 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051, ERS027646_01755, ERS027651_01374, ...Gene: rsmD, ERS007661_01921, ERS007663_00818, ERS007665_01852, ERS007672_04225, ERS007681_00248, ERS007722_02698, ERS007739_01109, ERS007741_03599, ERS023446_00051, ERS027646_01755, ERS027651_01374, ERS027652_01710, ERS027654_02036, ERS027656_00358, ERS027659_03553, ERS031537_04978, SAMEA2682864_00651, SAMEA2683035_02297
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A045IDU3, UniProt: I6XFS7*PLUS, 16S rRNA (guanine966-N2)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Potassium acetate, 100mM Tris (PH 7.4)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.74→100.8 Å / Num. obs: 57366 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.153 / Net I/σ(I): 5.6
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.019 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3777 / Rsym value: 0.669

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P9N

3p9n


Resolution: 1.74→50.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.466 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 1207 2.3 %RANDOM
Rwork0.21142 ---
obs0.21211 51856 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.349 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å2-0 Å2-0.16 Å2
2--1.33 Å20 Å2
3----2.46 Å2
Refinement stepCycle: 1 / Resolution: 1.74→50.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 343 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194065
X-RAY DIFFRACTIONr_bond_other_d0.0020.024008
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9685541
X-RAY DIFFRACTIONr_angle_other_deg1.05139105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83220.943159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46415618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0931560
X-RAY DIFFRACTIONr_chiral_restr0.1070.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02918
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3052.2412177
X-RAY DIFFRACTIONr_mcbond_other2.2992.242176
X-RAY DIFFRACTIONr_mcangle_it3.6183.3332712
X-RAY DIFFRACTIONr_mcangle_other3.6173.3342713
X-RAY DIFFRACTIONr_scbond_it3.1492.761887
X-RAY DIFFRACTIONr_scbond_other3.1482.7611888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9873.9422830
X-RAY DIFFRACTIONr_long_range_B_refined7.55918.8944625
X-RAY DIFFRACTIONr_long_range_B_other7.27818.5624498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 97 -
Rwork0.359 3777 -
obs--97.46 %

+
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