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- PDB-6ygs: tRNA-guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ygs
TitletRNA-guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-(methylamino)-4-(4-(trifluoromethyl)phenethyl)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / HOMODIMER
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
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Chem-OQQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization and 19F NMR reveal dimer disturbing inhibitors and conformational changes at dimer contacts
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)43,6304
Polymers43,0701
Non-polymers5603
Water5,549308
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2598
Polymers86,1402
Non-polymers1,1206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)84.974, 64.822, 71.464
Angle α, β, γ (deg.)90.000, 93.866, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 43069.828 Da / Num. of mol.: 1 / Mutation: T312K
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OQQ / 6-amino-2-(methylamino)-4-(4-(trifluoromethyl)phenethyl)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 6-azanyl-2-(methylamino)-4-[2-[4-(trifluoromethyl)phenyl]ethyl]-1,5-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 402.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3N6O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES pH 5.5, 0.5 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2018
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→42.39 Å / Num. obs: 69560 / % possible obs: 91.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.76
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 10987 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.4→42.39 Å / SU ML: 0.1249 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.4498
RfactorNum. reflection% reflection
Rfree0.1639 3478 5 %
Rwork0.1351 --
obs0.1365 69553 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.78 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 36 308 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762916
X-RAY DIFFRACTIONf_angle_d0.9243961
X-RAY DIFFRACTIONf_chiral_restr0.0682410
X-RAY DIFFRACTIONf_plane_restr0.0066587
X-RAY DIFFRACTIONf_dihedral_angle_d22.78021098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.25471250.23152378X-RAY DIFFRACTION83.74
1.42-1.440.23951410.19722677X-RAY DIFFRACTION92.55
1.44-1.460.22391370.18062608X-RAY DIFFRACTION92.02
1.46-1.490.20931390.16112650X-RAY DIFFRACTION92.2
1.49-1.510.19081370.14962592X-RAY DIFFRACTION90.45
1.51-1.540.20161370.14052611X-RAY DIFFRACTION91.17
1.54-1.570.18421370.1322604X-RAY DIFFRACTION90.94
1.57-1.60.16191340.12422536X-RAY DIFFRACTION89.3
1.6-1.630.14771330.12672538X-RAY DIFFRACTION87.6
1.63-1.660.18011210.12742283X-RAY DIFFRACTION78.98
1.66-1.70.15531350.12092565X-RAY DIFFRACTION90.15
1.7-1.740.17731430.12052720X-RAY DIFFRACTION95.34
1.74-1.790.17021450.11672751X-RAY DIFFRACTION95.26
1.79-1.840.13791450.11312759X-RAY DIFFRACTION95.65
1.84-1.90.16351430.11262726X-RAY DIFFRACTION95.51
1.9-1.970.12211450.11462750X-RAY DIFFRACTION95.26
1.97-2.050.16091430.11492715X-RAY DIFFRACTION94.64
2.05-2.140.13991420.11772691X-RAY DIFFRACTION94.09
2.14-2.260.1721420.12422707X-RAY DIFFRACTION94.53
2.26-2.40.17131430.12672720X-RAY DIFFRACTION94.02
2.4-2.580.16081410.12382682X-RAY DIFFRACTION92.59
2.58-2.840.17061360.13582583X-RAY DIFFRACTION89.21
2.84-3.260.14451290.13742438X-RAY DIFFRACTION84.25
3.26-4.10.13611510.13172877X-RAY DIFFRACTION98.7
4.1-42.390.19611540.16812914X-RAY DIFFRACTION98.4

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