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- PDB-5sw3: Crystal Structure of TGT in complex with 3-Pyridinecarboxylic aci... -

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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-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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Experimental details

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Experiment

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

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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,

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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

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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

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