[English] 日本語
Yorodumi
- PDB-8h0t: Crystal structure of MnmM from B. subtilis complexed with SAH (1.17 A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h0t
TitleCrystal structure of MnmM from B. subtilis complexed with SAH (1.17 A)
ComponentsPutative rRNA methylase YtqB
KeywordsTRANSFERASE / Methyltransferase / tRNA post-transcriptional modification / MnmC mnm5(s2)U
Function / homologytRNA (5-methylaminomethyl-2-thiouridylate)(34)-methyltransferase activity / tRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (mnm(5)s(2)U34)-methyltransferase
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsKim, J. / Lee, J. / Cho, G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification.
Authors: Cho, G. / Lee, J. / Kim, J.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative rRNA methylase YtqB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6382
Polymers22,2531
Non-polymers3841
Water3,441191
1
A: Putative rRNA methylase YtqB
hetero molecules

A: Putative rRNA methylase YtqB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2754
Polymers44,5072
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2990 Å2
ΔGint-15 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.555, 55.387, 60.592
Angle α, β, γ (deg.)90.00, 103.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

21A-505-

HOH

-
Components

#1: Protein Putative rRNA methylase YtqB


Mass: 22253.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: ytqB, BSU30490 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34614, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 25% w/v PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.16→37.59 Å / Num. obs: 41988 / % possible obs: 72.5 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 11.6
Reflection shellResolution: 1.16→1.3 Å / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2103 / CC1/2: 0.626 / Rpim(I) all: 0.493 / Rrim(I) all: 0.951

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSJan 10, 2022data reduction
STARANISOdata scaling
MOLREP11.9.02phasing
MxDCdata collection
PDB_EXTRACT3.27data extraction
Coot0.9.8.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PON

4pon


Resolution: 1.17→37.59 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16663 2049 4.9 %RANDOM
Rwork0.13489 ---
obs0.13642 39938 74.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å21.31 Å2
2---1.34 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.17→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 26 191 1633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121507
X-RAY DIFFRACTIONr_bond_other_d0.010.0161389
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.6492045
X-RAY DIFFRACTIONr_angle_other_deg0.5951.5733247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.86754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4610261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021697
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02272
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_it2.2981.177757
X-RAY DIFFRACTIONr_mcbond_other2.2921.176757
X-RAY DIFFRACTIONr_mcangle_it2.8771.769948
X-RAY DIFFRACTIONr_mcangle_other2.8761.768949
X-RAY DIFFRACTIONr_scbond_it3.9391.69750
X-RAY DIFFRACTIONr_scbond_other3.9391.69750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7552.3381098
X-RAY DIFFRACTIONr_long_range_B_refined5.45125.6561683
X-RAY DIFFRACTIONr_long_range_B_other5.44925.6441684
X-RAY DIFFRACTIONr_rigid_bond_restr6.64132896
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.175→1.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 7 -
Rwork0.267 173 -
obs--4.33 %

+
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