[English] 日本語
Yorodumi
- PDB-2det: Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2det
TitleCocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state
Components
  • tRNA
  • tRNA-specific 2-thiouridylase mnmA
KeywordsTransferase/RNA / Protein-RNA complex / Transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA-uridine 2-sulfurtransferase / sulfurtransferase complex / tRNA wobble position uridine thiolation / sulfurtransferase activity / tRNA binding / ATP binding / cytosol
Similarity search - Function
tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs ...tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / SH3 type barrels. / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsNumata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
CitationJournal: Nature / Year: 2006
Title: Snapshots of tRNA sulphuration via an adenylated intermediate
Authors: Numata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
History
DepositionFeb 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: tRNA
A: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8863
Polymers66,7902
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.537, 108.015, 211.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

#1: RNA chain tRNA


Mass: 24378.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription.
#2: Protein tRNA-specific 2-thiouridylase mnmA / RNA sulfuration enzyme MnmA


Mass: 42411.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P25745, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.33 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES-Na buffer (pH 7.5), 1.3-1.5M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES-Na11
2lithium sulfate11
3HEPES-Na12
4lithium sulfate12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.97904, 0.97931, 0.9760, 0.9820
SYNCHROTRONSPring-8 BL41XU21
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 15, 2005
ADSC QUANTUM 3152CCDJun 4, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.979311
30.9761
40.9821
511
ReflectionResolution: 3.4→50 Å / Num. obs: 28072 / % possible obs: 96.8 % / Redundancy: 10 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34.4
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4 / % possible all: 97

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.4→39.48 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 203041.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 758 4.8 %RANDOM
Rwork0.263 ---
obs0.263 15834 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.118676 e/Å3
Displacement parametersBiso mean: 83.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.05 Å20 Å20 Å2
2---17.52 Å20 Å2
3---7.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.4→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 1488 5 0 4354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 128 5 %
Rwork0.303 2443 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top

+
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://pdbjlvh1.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