[English] 日本語
Yorodumi
- PDB-4leq: tRNA guanine transglycosylase (TGT) in complex with Furanoside-Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4leq
TitletRNA guanine transglycosylase (TGT) in complex with Furanoside-Based lin-Benzoguanine 1
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Tim Barrel / GLYCOSYLTRANSFERASE / Zinc-BINDING / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-1WK / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas Mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.405 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: Chemistry / Year: 2015
Title: Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appended lin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT).
Authors: Barandun, L.J. / Ehrmann, F.R. / Zimmerli, D. / Immekus, F. / Giroud, M. / Grunenfelder, C. / Schweizer, W.B. / Bernet, B. / Betz, M. / Heine, A. / Klebe, G. / Diederich, F.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7456
Polymers43,0701
Non-polymers6755
Water7,710428
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49112
Polymers86,1402
Non-polymers1,35110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3240 Å2
ΔGint-17 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.623, 65.106, 70.357
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-855-

HOH

21A-868-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 43069.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas Mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

-
Non-polymers , 5 types, 433 molecules

#2: Chemical ChemComp-1WK / methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-beta-D-ribo-hexofuranoside


Mass: 390.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N6O5
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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.: 428 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 13% PEG 8000, 100mM MES, 1mM DTT, 10% DMSO, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 8, 2012 / Details: RH-COATED SILICON WITH INDIRECT WATER COOLING
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.405→50 Å / Num. all: 76331 / Num. obs: 76331 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 1.405→1.43 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3734 / Rsym value: 0.497 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PUD

1pud


Resolution: 1.405→40.876 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1485 3838 5.03 %random
Rwork0.1232 ---
obs0.1245 76328 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.405→40.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 42 428 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063110
X-RAY DIFFRACTIONf_angle_d1.1064220
X-RAY DIFFRACTIONf_dihedral_angle_d12.8561193
X-RAY DIFFRACTIONf_chiral_restr0.07446
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.405-1.42240.19671070.16752250X-RAY DIFFRACTION81
1.4224-1.44110.20911400.15322641X-RAY DIFFRACTION95
1.4411-1.46090.15511470.142631X-RAY DIFFRACTION95
1.4609-1.48170.18321290.13022665X-RAY DIFFRACTION95
1.4817-1.50390.15931280.12642655X-RAY DIFFRACTION95
1.5039-1.52740.1691400.11622622X-RAY DIFFRACTION95
1.5274-1.55240.14721340.11242671X-RAY DIFFRACTION96
1.5524-1.57920.16381400.10762625X-RAY DIFFRACTION96
1.5792-1.60790.15281360.10142667X-RAY DIFFRACTION96
1.6079-1.63880.13231380.10222700X-RAY DIFFRACTION96
1.6388-1.67230.13461430.09872663X-RAY DIFFRACTION96
1.6723-1.70860.13191340.09982719X-RAY DIFFRACTION97
1.7086-1.74840.14621520.10072673X-RAY DIFFRACTION97
1.7484-1.79210.15471560.10912665X-RAY DIFFRACTION97
1.7921-1.84060.13181400.10312686X-RAY DIFFRACTION97
1.8406-1.89470.14751410.1062686X-RAY DIFFRACTION97
1.8947-1.95590.14281510.10752725X-RAY DIFFRACTION97
1.9559-2.02580.14681400.1092707X-RAY DIFFRACTION98
2.0258-2.10690.12661440.10782719X-RAY DIFFRACTION98
2.1069-2.20280.14541560.1142715X-RAY DIFFRACTION98
2.2028-2.31890.13371530.11882747X-RAY DIFFRACTION98
2.3189-2.46420.17231590.12672712X-RAY DIFFRACTION98
2.4642-2.65440.13851580.13572744X-RAY DIFFRACTION98
2.6544-2.92140.16011270.13462800X-RAY DIFFRACTION99
2.9214-3.3440.15011400.13652770X-RAY DIFFRACTION99
3.344-4.21240.13371430.12672797X-RAY DIFFRACTION99
4.2124-40.89330.15791620.14482835X-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