[English] 日本語
Yorodumi
- PDB-6yfx: TGT Y330F mutant crystallised at pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yfx
TitleTGT Y330F mutant crystallised at pH 5.5
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
Similarity search - Function
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Mutation study on tRNA-guanine transglycosylase for catalysis Testing
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2113
Polymers43,0541
Non-polymers1582
Water5,026279
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4236
Polymers86,1082
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2400 Å2
ΔGint-11 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.575, 65.066, 71.404
Angle α, β, γ (deg.)90.000, 93.712, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 43053.828 Da / Num. of mol.: 1 / Mutation: T312K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES pH 5.5, 0.5 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.38→42.56 Å / Num. obs: 79276 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.69 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.87
Reflection shellResolution: 1.38→1.46 Å / Num. unique obs: 12689 / CC1/2: 0.85

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.38→42.56 Å / SU ML: 0.1222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.2516
RfactorNum. reflection% reflection
Rfree0.1631 3963 5 %
Rwork0.1407 --
obs0.1418 79270 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.47 Å2
Refinement stepCycle: LAST / Resolution: 1.38→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 7 279 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692861
X-RAY DIFFRACTIONf_angle_d0.92473882
X-RAY DIFFRACTIONf_chiral_restr0.0701407
X-RAY DIFFRACTIONf_plane_restr0.0061528
X-RAY DIFFRACTIONf_dihedral_angle_d23.51341043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.390.24691350.20642578X-RAY DIFFRACTION96.31
1.39-1.410.25121440.19292720X-RAY DIFFRACTION99.17
1.41-1.430.20541410.18282676X-RAY DIFFRACTION99.33
1.43-1.450.20051410.18222688X-RAY DIFFRACTION98.88
1.45-1.470.20861390.1682645X-RAY DIFFRACTION99.15
1.47-1.490.18941430.15042717X-RAY DIFFRACTION98.76
1.49-1.510.19511390.14782641X-RAY DIFFRACTION98.65
1.51-1.540.18361390.14362634X-RAY DIFFRACTION97.33
1.54-1.560.1891440.12862731X-RAY DIFFRACTION99.1
1.56-1.590.13681390.12372657X-RAY DIFFRACTION99.29
1.59-1.620.14011420.11952697X-RAY DIFFRACTION99.27
1.62-1.660.16691410.12122678X-RAY DIFFRACTION99.19
1.66-1.690.17151420.12232683X-RAY DIFFRACTION99.33
1.69-1.730.16511430.12042720X-RAY DIFFRACTION99.51
1.73-1.780.14681420.11912713X-RAY DIFFRACTION99.65
1.78-1.820.1551420.12042688X-RAY DIFFRACTION98.88
1.82-1.880.15231400.12352657X-RAY DIFFRACTION98.42
1.88-1.940.13331400.12332665X-RAY DIFFRACTION97.94
1.94-2.010.15561420.12372688X-RAY DIFFRACTION99.44
2.01-2.090.15251430.12182722X-RAY DIFFRACTION99.58
2.09-2.180.11131430.12012712X-RAY DIFFRACTION99.48
2.18-2.30.16181430.12682722X-RAY DIFFRACTION99.51
2.3-2.440.16051420.12712703X-RAY DIFFRACTION99.55
2.44-2.630.15221420.13572698X-RAY DIFFRACTION98.37
2.63-2.90.14821400.14242656X-RAY DIFFRACTION97.63
2.9-3.310.16111440.13972738X-RAY DIFFRACTION99.65
3.31-4.170.16171440.14352732X-RAY DIFFRACTION99.07
4.17-42.560.19691440.18182748X-RAY DIFFRACTION97.77

+
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