[English] 日本語
Yorodumi
- PDB-7nzj: Structure of bsTrmB apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nzj
TitleStructure of bsTrmB apo
ComponentstRNA (guanine-N(7)-)-methyltransferase
KeywordsRNA BINDING PROTEIN / m7G Methyltransferase / Rossman-like fold / tRNA modifying enzyme
Function / homology
Function and homology information


RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation
Similarity search - Function
: / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBlersch, K.F. / Ficner, R. / Neumann, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Rna Biol. / Year: 2021
Title: Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA.
Authors: Blersch, K.F. / Burchert, J.P. / August, S.C. / Welp, L. / Neumann, P. / Koster, S. / Urlaub, H. / Ficner, R.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase
C: tRNA (guanine-N(7)-)-methyltransferase
D: tRNA (guanine-N(7)-)-methyltransferase
E: tRNA (guanine-N(7)-)-methyltransferase
F: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,71012
Polymers147,2266
Non-polymers4836
Water16,430912
1
A: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1914
Polymers49,0752
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area19090 Å2
MethodPISA
2
C: tRNA (guanine-N(7)-)-methyltransferase
D: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3525
Polymers49,0752
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-6 kcal/mol
Surface area18780 Å2
MethodPISA
3
E: tRNA (guanine-N(7)-)-methyltransferase
F: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1683
Polymers49,0752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-6 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 103.680, 103.690
Angle α, β, γ (deg.)118.120, 97.910, 97.840
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
tRNA (guanine-N(7)-)-methyltransferase / BsTrmB / tRNA (guanine(46)-N(7))-methyltransferase / tRNA(m7G46)-methyltransferase


Mass: 24537.744 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: trmB, ytmQ, BSU29900 / Production host: Escherichia coli (E. coli)
References: UniProt: O34522, tRNA (guanine46-N7)-methyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M NaCl, 0.1M MES, 15% v/v 5/4PO/OH,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→44.53 Å / Num. obs: 96395 / % possible obs: 91.5 % / Redundancy: 3.861 % / Biso Wilson estimate: 42.408 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Χ2: 0.85 / Net I/σ(I): 12.47 / Num. measured all: 372163 / Scaling rejects: 51
Reflection shellResolution: 1.98→2 Å / Redundancy: 3.896 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2799 / CC1/2: 0.548 / Rrim(I) all: 1.557 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FCA

2fca


Resolution: 1.98→44.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2146 / WRfactor Rwork: 0.1808 / FOM work R set: 0.7547 / SU B: 5.5 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1853 / SU Rfree: 0.1594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 5048 5.2 %RANDOM
Rwork0.1874 ---
obs0.1893 91357 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 41.456 Å2 / Biso min: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å2-0.47 Å2-0.36 Å2
2---1.71 Å20.31 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.98→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9925 0 31 912 10868
Biso mean--55.27 48.42 -
Num. residues----1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310182
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179503
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.64213749
X-RAY DIFFRACTIONr_angle_other_deg2.2321.58721941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21751222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09623.768552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.695151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9531542
X-RAY DIFFRACTIONr_chiral_restr0.070.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211572
X-RAY DIFFRACTIONr_gen_planes_other0.010.022368
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 315 -
Rwork0.341 6866 -
all-7181 -
obs--90.47 %

+
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