[English] 日本語
Yorodumi
- PDB-5wt1: Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cogn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wt1
TitlePyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA
Components
  • RNA (76-MER)
  • tRNA (guanine(37)-N1)-methyltransferase Trm5a
KeywordsTRANSFERASE/RNA / methyltransferase / Trm5a / wyosine hypermodification / TRANSFERASE-RNA complex
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
SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / tRNA (guanine(37)-N1)/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsXie, W. / Wang, C. / Jia, Q.
CitationJournal: Sci Adv / Year: 2017
Title: Structural insight into the methyltransfer mechanism of the bifunctional Trm5.
Authors: Wang, C. / Jia, Q. / Zeng, J. / Chen, R. / Xie, W.
History
DepositionDec 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 8, 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: tRNA (guanine(37)-N1)-methyltransferase Trm5a
C: RNA (76-MER)
B: tRNA (guanine(37)-N1)-methyltransferase Trm5a
F: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9626
Polymers126,1934
Non-polymers7692
Water1,08160
1
A: tRNA (guanine(37)-N1)-methyltransferase Trm5a
C: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4813
Polymers63,0972
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-32 kcal/mol
Surface area23250 Å2
MethodPISA
2
B: tRNA (guanine(37)-N1)-methyltransferase Trm5a
F: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4813
Polymers63,0972
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.096, 57.017, 115.807
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number3
Space group name H-MP121

-
Components

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


Mass: 38545.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase
#2: RNA chain RNA (76-MER)


Mass: 24551.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) / References: GenBank: HE613800.1
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 45% MPD, 100 mM MES (pH 6.5), 200 mM NH4OAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.598→50 Å / Num. obs: 40587 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.739 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZN

2zzn


Resolution: 2.598→40.217 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 2020 5.01 %
Rwork0.2474 --
obs0.2488 40281 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→40.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 2895 52 60 7973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058348
X-RAY DIFFRACTIONf_angle_d0.97612002
X-RAY DIFFRACTIONf_dihedral_angle_d14.9134706
X-RAY DIFFRACTIONf_chiral_restr0.0561491
X-RAY DIFFRACTIONf_plane_restr0.0071040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5978-2.66280.45341470.38092484X-RAY DIFFRACTION92
2.6628-2.73470.41751210.35072769X-RAY DIFFRACTION100
2.7347-2.81520.38591290.34492749X-RAY DIFFRACTION100
2.8152-2.9060.38811430.34882748X-RAY DIFFRACTION100
2.906-3.00990.36331740.31342740X-RAY DIFFRACTION100
3.0099-3.13030.36611390.3052734X-RAY DIFFRACTION100
3.1303-3.27270.30961290.2692708X-RAY DIFFRACTION99
3.2727-3.44520.2771510.26132737X-RAY DIFFRACTION99
3.4452-3.66090.28211660.26032739X-RAY DIFFRACTION100
3.6609-3.94330.27571500.23492746X-RAY DIFFRACTION100
3.9433-4.33980.23341370.22262783X-RAY DIFFRACTION100
4.3398-4.96670.21641380.2122766X-RAY DIFFRACTION99
4.9667-6.25380.23511420.2252800X-RAY DIFFRACTION100
6.2538-40.22180.24351540.21152758X-RAY DIFFRACTION96

+
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