[English] 日本語
Yorodumi
- PDB-8sh4: Crystal structure of the tRNA (m1G37) methyltransferase apoenzyme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sh4
TitleCrystal structure of the tRNA (m1G37) methyltransferase apoenzyme from Anaplasma phagocytophilum
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / methyltransferase / apoenzyme / TrmD / SPOUT
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm
Similarity search - Function
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase TrmD / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Picchiello, C. / Collins, K. / Garland, E. / Handley-Pendleton, J. ...Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Picchiello, C. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. / Perez, A. / Halloran, J. / Bolen, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
Department of Energy (DOE, United States)KP1605010 United States
CitationJournal: To Be Published
Title: Crystal structure of the m1G37 tRNA methyltransferase apoenzyme from Anaplasma phagocytophilum
Authors: Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. ...Authors: Jannotta, C. / Edele, D. / Levanti, D. / Carson, M. / Prucha, G. / Caesar, J. / Collins, K. / Garland, E. / Handley-Pendleton, J. / Hernandez, V. / Leffler, S. / Williams, D. / Stojanoff, V. / Perez, A. / Halloran, J. / Bolen, R.
History
DepositionApr 13, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2024ID: 6UEV
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1622
Polymers24,0701
Non-polymers921
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.730, 104.730, 91.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase


Mass: 24069.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Gene: trmD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182A739
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.83 Å3/Da / Density % sol: 74.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 8% PEG 3350, 0.5mL of 0.1M sodium citrate, 10% glycerol, ethylene glycol as cryoprotectant

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.676→34.4 Å / Num. obs: 11321 / % possible obs: 88.49 % / Redundancy: 15.5 % / Biso Wilson estimate: 77.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.3
Reflection shellResolution: 2.676→2.854 Å / Num. unique obs: 566 / CC1/2: 0.535

-
Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KNU

3knu


Resolution: 2.9→34.4 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 506 4.88 %
Rwork0.2016 --
obs0.2041 10377 88.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 6 24 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091680
X-RAY DIFFRACTIONf_angle_d1.132285
X-RAY DIFFRACTIONf_dihedral_angle_d6.397237
X-RAY DIFFRACTIONf_chiral_restr0.054261
X-RAY DIFFRACTIONf_plane_restr0.008298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.3312850.29221629X-RAY DIFFRACTION60
3.19-3.650.30251380.22912533X-RAY DIFFRACTION92
3.65-4.60.22821350.18532782X-RAY DIFFRACTION100
4.6-34.40.24491480.19132927X-RAY DIFFRACTION100

+
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