[English] 日本語
Yorodumi
- PDB-5hjm: Crystal Structure of Pyrococcus abyssi Trm5a complexed with MTA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hjm
TitleCrystal Structure of Pyrococcus abyssi Trm5a complexed with MTA
ComponentstRNA (guanine(37)-N1)-methyltransferase Trm5a
KeywordsTRANSFERASE / Methyltransferase / Trm5a / SAM / tRNA modification
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm
Similarity search - Function
Met-10+ protein-like domains / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / GMP Synthetase; Chain A, domain 3 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HOMOSERINE LACTONE / 5'-DEOXY-5'-METHYLTHIOADENOSINE / tRNA (guanine(37)-N1)/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsXie, W. / Wang, C. / Jia, Q.
Funding support China, 3items
OrganizationGrant numberCountry
Guangdong Innovative Research Team2011Y038 China
Science and Technology Program of Guangzhou201504010025 China
Fundamental Research Funds for the Central Universities15lgjc02 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures of the bifunctional tRNA methyltransferase Trm5a
Authors: Wang, C. / Jia, Q. / Chen, R. / Wei, Y. / Li, J. / Ma, J. / Xie, W.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (guanine(37)-N1)-methyltransferase Trm5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2164
Polymers40,7591
Non-polymers4573
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-2 kcal/mol
Surface area19610 Å2
Unit cell
Length a, b, c (Å)52.969, 55.334, 130.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein tRNA (guanine(37)-N1)-methyltransferase Trm5a / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 40758.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H15N5O3S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HSL / HOMOSERINE LACTONE / N-Acyl homoserine lactone


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.57 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-15% PEG3350, 100mM HEPES, pH7.5, 100mM Ca(OAc)2 and 100mM KCl
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 38919 / % possible obs: 99.4 % / Observed criterion σ(I): 6.5 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.1
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 6.5 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJK

5hjk


Resolution: 1.762→36.72 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2028 1880 4.87 %
Rwork0.1761 --
obs0.1775 38622 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.762→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 31 408 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042929
X-RAY DIFFRACTIONf_angle_d0.8973951
X-RAY DIFFRACTIONf_dihedral_angle_d13.1461134
X-RAY DIFFRACTIONf_chiral_restr0.035446
X-RAY DIFFRACTIONf_plane_restr0.003503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7616-1.80920.30121200.22112754X-RAY DIFFRACTION98
1.8092-1.86250.25421370.19812808X-RAY DIFFRACTION100
1.8625-1.92260.24821240.19282797X-RAY DIFFRACTION100
1.9226-1.99130.23521410.18942798X-RAY DIFFRACTION100
1.9913-2.0710.221400.18242806X-RAY DIFFRACTION100
2.071-2.16520.21391570.18272780X-RAY DIFFRACTION100
2.1652-2.27940.21121340.18312815X-RAY DIFFRACTION100
2.2794-2.42220.25831390.18852843X-RAY DIFFRACTION100
2.4222-2.60910.23081650.1862801X-RAY DIFFRACTION100
2.6091-2.87160.19241600.18282802X-RAY DIFFRACTION100
2.8716-3.28690.22361610.18162863X-RAY DIFFRACTION100
3.2869-4.14030.17331440.15912886X-RAY DIFFRACTION100
4.1403-36.72290.16171580.15942989X-RAY DIFFRACTION99

+
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