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- PDB-6fso: Crystal Structure of TGT in complex with methyl({[5-(pyridin-3-yl... -

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Basic information

Entry
Database: PDB / ID: 6fso
TitleCrystal Structure of TGT in complex with methyl({[5-(pyridin-3-yloxy)furan-2-yl]methyl})amine
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-guanine transglycosylation / queuosine 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
ACETATE ION / Chem-F63 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 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
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 2.0May 8, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 2.1Jun 26, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 2.2Mar 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 2.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,83310
Polymers41,7631
Non-polymers1,0709
Water4,540252
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,66620
Polymers83,5272
Non-polymers2,13918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)90.460, 64.713, 70.552
Angle α, β, γ (deg.)90.00, 95.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

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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)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 8 types, 261 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-F63 / N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine


Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.449→43.289 Å / Num. obs: 68288 / % possible obs: 94.8 % / Redundancy: 2.68 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 9.82
Reflection shellResolution: 1.449→1.54 Å

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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: 1.449→43.289 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 3409 5 %
Rwork0.1658 --
obs0.1668 68178 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.449→43.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 68 252 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083010
X-RAY DIFFRACTIONf_angle_d0.9894043
X-RAY DIFFRACTIONf_dihedral_angle_d22.8181143
X-RAY DIFFRACTIONf_chiral_restr0.073421
X-RAY DIFFRACTIONf_plane_restr0.007547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4488-1.46950.42461370.34392587X-RAY DIFFRACTION90
1.4695-1.49140.33991390.312654X-RAY DIFFRACTION94
1.4914-1.51470.2731440.28962725X-RAY DIFFRACTION96
1.5147-1.53950.32851320.30862509X-RAY DIFFRACTION87
1.5395-1.56610.2371430.21972710X-RAY DIFFRACTION97
1.5661-1.59460.24161450.19072746X-RAY DIFFRACTION97
1.5946-1.62520.19551460.17822779X-RAY DIFFRACTION97
1.6252-1.65840.20991430.17612729X-RAY DIFFRACTION97
1.6584-1.69450.17951460.172773X-RAY DIFFRACTION98
1.6945-1.73390.21621460.17112760X-RAY DIFFRACTION97
1.7339-1.77730.18551440.15022751X-RAY DIFFRACTION98
1.7773-1.82530.151460.14492769X-RAY DIFFRACTION97
1.8253-1.8790.17811460.15232764X-RAY DIFFRACTION97
1.879-1.93970.22251280.192440X-RAY DIFFRACTION86
1.9397-2.0090.14831430.152714X-RAY DIFFRACTION96
2.009-2.08940.18661340.16942571X-RAY DIFFRACTION90
2.0894-2.18450.15671460.13872766X-RAY DIFFRACTION97
2.1845-2.29970.21961330.15932540X-RAY DIFFRACTION89
2.2997-2.44380.14721460.1292778X-RAY DIFFRACTION97
2.4438-2.63240.15871460.13532777X-RAY DIFFRACTION97
2.6324-2.89730.16311390.14572633X-RAY DIFFRACTION92
2.8973-3.31640.15671460.15052782X-RAY DIFFRACTION97
3.3164-4.17780.15941410.15142670X-RAY DIFFRACTION93
4.1778-43.3080.18531500.16492842X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4312-0.13980.1772-0.01540.03990.2997-0.009-0.01890.005-0.01180.0032-0.01060.0251-0.0389-0.01020.06840.0011-0.00260.06990.00240.073392.13959.799488.5334
20.04590.0316-0.03790.02-0.03480.0357-0.080.0230.1909-0.24060.00680.0416-0.1424-0.1138-0.01660.26790.0466-0.13010.1418-0.05450.213188.310632.805196.5121
30.10580.01980.13120.02370.01210.1414-0.0021-0.16460.13460.0505-0.02610.01370.0327-0.08030.00110.07680.0016-0.00710.1052-0.03260.102490.630119.607699.462
40.2733-0.04050.24650.36470.24810.4426-0.0318-0.12090.0396-0.00840.0399-0.0657-0.05430.03840.01860.0958-0.00290.00130.0913-0.03270.0947103.249619.9772102.3205
50.2443-0.1162-0.12470.29160.27220.25780.0253-0.020.0937-0.04930.0507-0.0697-0.0440.08980.01490.0814-0.00210.00640.0674-0.00960.109109.639216.068887.7626
60.0021-0.20820.26330.0295-0.27440.5042-0.01120.06550.0082-0.0254-0.0159-0.03930.02320.05470.00260.076-0.00170.00260.0830.01120.0834101.156812.163768.0324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 284 )
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 383 )

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