[English] 日本語
Yorodumi
- PDB-5j9o: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j9o
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 1-(2-(methylamino)-1H-benzo[d]imidazol-6-yl)guanidine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Benzimidazole-derivatives / shigellosis / TRANSFERASE INHIBITOR
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
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
N-[2-(methylamino)-1H-benzimidazol-6-yl]guanidine / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines.
Authors: Ehrmann, F.R. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionApr 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_special_symmetry
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)43,4156
Polymers42,9261
Non-polymers4895
Water5,260292
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,83012
Polymers85,8512
Non-polymers97910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4610 Å2
ΔGint-43 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.102, 63.798, 70.955
Angle α, β, γ (deg.)90.00, 92.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-773-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 42925.703 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)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

-
Non-polymers , 5 types, 297 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-6H8 / N-[2-(methylamino)-1H-benzimidazol-6-yl]guanidine


Mass: 204.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N6
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 48.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.41→19.45 Å / Num. obs: 76131 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rsym value: 0.035 / Net I/σ(I): 16.88
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.26 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1492)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.41→19.45 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.74
RfactorNum. reflection% reflection
Rfree0.1693 3805 5 %
Rwork0.1399 --
obs0.1414 76103 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.41→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 29 292 3175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053085
X-RAY DIFFRACTIONf_angle_d0.7764172
X-RAY DIFFRACTIONf_dihedral_angle_d20.7631163
X-RAY DIFFRACTIONf_chiral_restr0.07434
X-RAY DIFFRACTIONf_plane_restr0.006577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.42560.28311290.24872461X-RAY DIFFRACTION90
1.4256-1.44430.22671400.22632670X-RAY DIFFRACTION97
1.4443-1.46410.22091380.19652605X-RAY DIFFRACTION97
1.4641-1.4850.2131400.18172660X-RAY DIFFRACTION97
1.485-1.50720.20651380.16992620X-RAY DIFFRACTION97
1.5072-1.53070.21331410.15622687X-RAY DIFFRACTION97
1.5307-1.55580.17381380.14892621X-RAY DIFFRACTION97
1.5558-1.58260.20411400.13812649X-RAY DIFFRACTION98
1.5826-1.61140.15921410.12952689X-RAY DIFFRACTION98
1.6114-1.64240.17921400.12352653X-RAY DIFFRACTION98
1.6424-1.67590.15321420.12712689X-RAY DIFFRACTION98
1.6759-1.71230.18121380.12382639X-RAY DIFFRACTION98
1.7123-1.75210.1741400.12852667X-RAY DIFFRACTION98
1.7521-1.79590.16511420.13092692X-RAY DIFFRACTION98
1.7959-1.84440.15371420.12872696X-RAY DIFFRACTION98
1.8444-1.89860.18021410.12612680X-RAY DIFFRACTION98
1.8986-1.95990.16751410.12742690X-RAY DIFFRACTION99
1.9599-2.02990.15081430.12872715X-RAY DIFFRACTION99
2.0299-2.1110.16821420.13582688X-RAY DIFFRACTION99
2.111-2.2070.18051420.13332710X-RAY DIFFRACTION99
2.207-2.32320.1661420.13262687X-RAY DIFFRACTION99
2.3232-2.46840.1571420.14032706X-RAY DIFFRACTION99
2.4684-2.65860.17231440.14842726X-RAY DIFFRACTION99
2.6586-2.92530.16861430.14922724X-RAY DIFFRACTION99
2.9253-3.34680.1691430.14512720X-RAY DIFFRACTION99
3.3468-4.20950.15911460.13232769X-RAY DIFFRACTION99
4.2095-19.450.16641470.14042785X-RAY DIFFRACTION99

+
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