[English] 日本語
Yorodumi
- PDB-6emv: Crystal Structure of dual specific Trm10 construct from Thermococ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6emv
TitleCrystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.
ComponentstRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
KeywordsRNA BINDING PROTEIN / Trm10 / Dual specificity enzymes / SPOUT / MTases
Function / homology
Function and homology information


tRNA (adenine9-N1)-methyltransferase / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA (guanine9-N1)-methyltransferase / tRNA (guanosine(9)-N1)-methyltransferase activity / tRNA methylation / tRNA processing / cytoplasm
Similarity search - Function
: / Protein arginine N-methyltransferase SFM1-like / tRNA methyltransferase, archaea / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile.
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.90001435892 Å
AuthorsSingh, R.K. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek (FWO) Belgium
CitationJournal: RNA / Year: 2018
Title: Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.
Authors: Singh, R.K. / Feller, A. / Roovers, M. / Van Elder, D. / Wauters, L. / Droogmans, L. / Versees, W.
History
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: 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(9)-/adenine(9)-N1)-methyltransferase
B: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
C: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4216
Polymers67,2683
Non-polymers1,1533
Water41423
1
A: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8072
Polymers22,4231
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8072
Polymers22,4231
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8072
Polymers22,4231
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.082, 71.082, 192.233
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

-
Components

#1: Protein tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase / tRNA(m1G9/m1A9)-methyltransferase / tRNA(m1G9/m1A9)MTase


Mass: 22422.598 Da / Num. of mol.: 3 / Mutation: C120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0422 / Plasmid: pet28b
Details (production host): bactrerial expression vector with T7 lac promotor
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q5JD38, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 10% PEG6000, 0.2M LiCl and 0.1M NaAc pH 5.5 / PH range: 5.4-5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.9→44.3924298364 Å / Num. obs: 12193 / % possible obs: 99.87 % / Redundancy: 9.1 % / Biso Wilson estimate: 64.104975072 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1927 / Rpim(I) all: 0.06787 / Rrim(I) all: 0.2044 / Net I/σ(I): 9.88
Reflection shellResolution: 2.9→2.999 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 1223 / CC1/2: 0.659 / Rpim(I) all: 0.3976 / Rrim(I) all: 1.203 / % possible all: 99.67

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDS2015-10-15data reduction
XDS2015-10-15data scaling
PHASER2.5.5phasing
RefinementStarting model: previously solved structure ( unpublished)

Resolution: 2.90001435892→44.3924298364 Å / SU ML: 0.372762584057 / Cross valid method: THROUGHOUT / σ(F): 1.36606548727 / Phase error: 28.2855881253
RfactorNum. reflection% reflectionSelection details
Rfree0.250478342492 609 4.99835850295 %RANDOM
Rwork0.19354637844 ---
obs0.196476138728 12184 99.9016070843 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.8643381185 Å2
Refinement stepCycle: LAST / Resolution: 2.90001435892→44.3924298364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 78 23 4087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001885387036524152
X-RAY DIFFRACTIONf_angle_d0.4778055603275619
X-RAY DIFFRACTIONf_chiral_restr0.0452164614726632
X-RAY DIFFRACTIONf_plane_restr0.00245607741186705
X-RAY DIFFRACTIONf_dihedral_angle_d13.56582597272466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.19180.317121436531540.257109111062913X-RAY DIFFRACTION99.9674054759
3.1918-3.65340.2999603502251500.2289787897072858X-RAY DIFFRACTION99.8671978752
3.6534-4.60220.2337566234551520.1749025946552894X-RAY DIFFRACTION100
4.6022-44.39760.2204000493251530.1740832497532910X-RAY DIFFRACTION99.8370273794
Refinement TLS params.Method: refined / Origin x: 9.44406590351 Å / Origin y: -26.0576400615 Å / Origin z: -17.2129730769 Å
111213212223313233
T0.349525671925 Å2-0.0718328180412 Å2-0.041637292696 Å2-0.310137384779 Å20.025096727051 Å2--0.393416395247 Å2
L0.96463959736 °2-0.20984471308 °2-0.188479929671 °2-0.138642199465 °20.0161517741612 °2--1.28119466499 °2
S-0.0287748172678 Å °0.12792370762 Å °0.119846748779 Å °-0.0449317727112 Å °0.051529079538 Å °-0.0479314177077 Å °0.0251929036556 Å °-0.068248699791 Å °-0.0301996523934 Å °
Refinement TLS groupSelection details: all

+
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