[English] 日本語
Yorodumi
- PDB-5sw3: Crystal Structure of TGT in complex with 3-Pyridinecarboxylic aci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sw3
TitleCrystal Structure of TGT in complex with 3-Pyridinecarboxylic acid, 6-(dimethylamino)
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA / GUANINE EXCHANGE ENZYME / PROTEIN INTERFACE
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
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-(dimethylamino)pyridine-3-carboxylic acid / DI(HYDROXYETHYL)ETHER / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2020
Title: Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies.
Authors: Hassaan, E. / Eriksson, P.O. / Geschwindner, S. / Heine, A. / Klebe, G.
History
DepositionAug 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6969
Polymers41,7631
Non-polymers9338
Water4,017223
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,39218
Polymers83,5272
Non-polymers1,86516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4930 Å2
ΔGint-2 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.027, 64.071, 70.453
Angle α, β, γ (deg.)90.00, 92.82, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 41763.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Gene: tgt, ZMO0363 / Plasmid: PPR-IBA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

-
Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-46L / 6-(dimethylamino)pyridine-3-carboxylic acid


Mass: 166.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N2O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 13% PEG 8000, 100MM MES, 1MM DTT, 10% DMSO,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→44.46 Å / Num. obs: 81197 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rsym value: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.47 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LBU

4lbu


Resolution: 1.38→44.46 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 4060 5 %
Rwork0.1332 --
obs0.1346 81188 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 57 223 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073002
X-RAY DIFFRACTIONf_angle_d0.9444055
X-RAY DIFFRACTIONf_dihedral_angle_d21.3881125
X-RAY DIFFRACTIONf_chiral_restr0.071429
X-RAY DIFFRACTIONf_plane_restr0.006553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3788-1.3950.23851330.21922529X-RAY DIFFRACTION96
1.395-1.4120.24321400.19262656X-RAY DIFFRACTION100
1.412-1.42990.22511390.18642651X-RAY DIFFRACTION100
1.4299-1.44870.23591390.17312632X-RAY DIFFRACTION100
1.4487-1.46860.20391390.16322649X-RAY DIFFRACTION100
1.4686-1.48950.19871420.15362691X-RAY DIFFRACTION100
1.4895-1.51180.17651390.14692645X-RAY DIFFRACTION100
1.5118-1.53540.18811390.14422643X-RAY DIFFRACTION100
1.5354-1.56060.17321410.13272665X-RAY DIFFRACTION100
1.5606-1.58750.14891370.12552615X-RAY DIFFRACTION100
1.5875-1.61640.12381410.112677X-RAY DIFFRACTION100
1.6164-1.64740.1721400.10962653X-RAY DIFFRACTION100
1.6474-1.68110.15581420.11112695X-RAY DIFFRACTION100
1.6811-1.71760.13541390.11142643X-RAY DIFFRACTION100
1.7176-1.75760.14761380.11132637X-RAY DIFFRACTION100
1.7576-1.80150.1571400.10542658X-RAY DIFFRACTION100
1.8015-1.85020.14691410.11172667X-RAY DIFFRACTION100
1.8502-1.90470.13051400.11322673X-RAY DIFFRACTION100
1.9047-1.96620.15791400.11492654X-RAY DIFFRACTION100
1.9662-2.03640.16511410.11252672X-RAY DIFFRACTION100
2.0364-2.1180.16191390.11352650X-RAY DIFFRACTION100
2.118-2.21440.14071420.11032686X-RAY DIFFRACTION100
2.2144-2.33110.13111390.11092648X-RAY DIFFRACTION100
2.3311-2.47720.14251410.1182669X-RAY DIFFRACTION100
2.4772-2.66840.15991400.1272664X-RAY DIFFRACTION100
2.6684-2.93690.16131410.13632679X-RAY DIFFRACTION100
2.9369-3.36170.1491420.1472694X-RAY DIFFRACTION100
3.3617-4.23490.16591410.14382689X-RAY DIFFRACTION100
4.2349-44.48290.18831450.16512744X-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