[English] 日本語
Yorodumi
- PDB-3a4t: Crystal structure of aTrm4 from M.jannaschii with sinefungin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a4t
TitleCrystal structure of aTrm4 from M.jannaschii with sinefungin
ComponentsPutative methyltransferase MJ0026
KeywordsTRANSFERASE / tRNA / m5C / Rossmann fold / Structural Genomics / RSGI / RIKEN Structural Genomics/Proteomics Initiative / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


tRNA (cytidine-5-)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm
Similarity search - Function
Sun protein; domain 3 / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 ...Sun protein; domain 3 / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / tRNA (cytosine(48)-C(5))-methyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHirano, M. / Kuratani, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
Authors: Kuratani, M. / Hirano, M. / Goto-Ito, S. / Itoh, Y. / Hikida, Y. / Nishimoto, M. / Sekine, S. / Bessho, Y. / Ito, T. / Grosjean, H. / Yokoyama, S.
History
DepositionJul 14, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative methyltransferase MJ0026
B: Putative methyltransferase MJ0026
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8334
Polymers63,0702
Non-polymers7632
Water3,009167
1
A: Putative methyltransferase MJ0026
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9172
Polymers31,5351
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative methyltransferase MJ0026
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9172
Polymers31,5351
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.259, 40.097, 85.951
Angle α, β, γ (deg.)90.00, 110.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-276-

HOH

-
Components

#1: Protein Putative methyltransferase MJ0026


Mass: 31535.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0026 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q60343, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100mM Tris-HCl buffer (pH 7.4) , 200mM MgCl2 ,25% PEG 3350, 10mM cytidine, 3mM sinefungin, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.45 Å / Num. obs: 24668 / % possible obs: 1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.022 / Rsym value: 0.024 / Net I/σ(I): 19.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 0.488 / Num. unique all: 2457 / Rsym value: 0.627 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A1X

3a1x
PDB Unreleased entry


Resolution: 2.3→42.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.269 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.361 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26756 1248 5.1 %RANDOM
Rwork0.18116 ---
all0.18551 23355 --
obs0.18551 23309 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.653 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 54 167 4332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224237
X-RAY DIFFRACTIONr_angle_refined_deg2.2842.0155702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7125507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.525.057174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05215849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1991520
X-RAY DIFFRACTIONr_chiral_restr0.1540.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023034
X-RAY DIFFRACTIONr_nbd_refined0.2280.22080
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.211
X-RAY DIFFRACTIONr_mcbond_it1.1631.52672
X-RAY DIFFRACTIONr_mcangle_it1.84324177
X-RAY DIFFRACTIONr_scbond_it3.38631815
X-RAY DIFFRACTIONr_scangle_it5.0294.51525
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 118 -
Rwork0.205 1700 -
obs-1700 99.95 %

+
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