[English] 日本語
Yorodumi
- PDB-6zmb: Structure of the native tRNA-Monooxygenase enzyme MiaE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zmb
TitleStructure of the native tRNA-Monooxygenase enzyme MiaE
ComponentstRNA hydroxylase
KeywordsOXIDOREDUCTASE / tRNA-monooxygenase metallo-enzyme tRNA-modifying enzyme hydroxylase
Function / homology
Function and homology information


tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity / tRNA modification / metal ion binding
Similarity search - Function
tRNA-hydroxylase MiaE / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL / tRNA-(Ms[2]io[6]A)-hydroxylase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCarpentier, P. / Atta, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE21-0020 France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction.
Authors: Carpentier, P. / Lepretre, C. / Basset, C. / Douki, T. / Torelli, S. / Duarte, V. / Hamdane, D. / Fontecave, M. / Atta, M.
History
DepositionJul 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: tRNA hydroxylase
C: tRNA hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,87417
Polymers45,3222
Non-polymers1,55215
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-47 kcal/mol
Surface area16670 Å2
Unit cell
Length a, b, c (Å)116.797, 50.929, 76.258
Angle α, β, γ (deg.)90.000, 91.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

21B-426-

HOH

31B-481-

HOH

41B-485-

HOH

51B-491-

HOH

-
Components

-
Protein , 1 types, 2 molecules BC

#1: Protein tRNA hydroxylase / tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) / tRNA-(Ms[2]io[6]A)-hydroxylase


Mass: 22661.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_21560, CBL13_00280, CBP06_18695 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A179QS89

-
Non-polymers , 9 types, 232 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 % / Description: elongated
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MiaE: 20 mg/ml in 100 mM HEPES, pH 7.5, 30mM NaCl reservoir solution: 0.5M CaCl2, 42% PEG 6k, 2M Tris-Cl pH 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9753 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 48290 / % possible obs: 97.5 % / Observed criterion σ(I): 1.44 / Redundancy: 2.8 % / Biso Wilson estimate: 38.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.04 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.8 % / Num. unique obs: 7733 / CC1/2: 0.845 / Rrim(I) all: 0.846 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.1refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ITB

2itb


Resolution: 1.7→46.752 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2501 5.19 %
Rwork0.1881 --
obs0.1897 48185 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 36.955 Å2 / Biso min: 18.88 Å2
Refinement stepCycle: final / Resolution: 1.7→46.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 88 217 3460
Biso mean--47.74 46.84 -
Num. residues----399
LS refinement shellResolution: 1.7→1.73 Å /
RfactorNum. reflection
Rfree0.396 -
Rwork0.365 -
obs-2454

+
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