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- PDB-6yh1: tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptoph... -

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Basic information

Entry
Database: PDB / ID: 6yh1
TitletRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan 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 / 19F NMR
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
: / 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 ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization, nanoESI-MS and 19F NMR reveal dimer disturbing inhibitors and conformational changes at dimer contacts
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionMar 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6103
Polymers43,1421
Non-polymers4682
Water5,693316
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2196
Polymers86,2842
Non-polymers9364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2260 Å2
ΔGint-15 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.872, 65.286, 71.982
Angle α, β, γ (deg.)90.000, 94.041, 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: 43141.789 Da / Num. of mol.: 1 / Mutation: T312K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
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: Jan 18, 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: 1.55→42.96 Å / Num. obs: 55401 / % possible obs: 96.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.68
Reflection shellResolution: 1.55→1.65 Å / Num. unique obs: 8137 / CC1/2: 0.918

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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: 1.55→42.96 Å / SU ML: 0.1609 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.1004
RfactorNum. reflection% reflection
Rfree0.1673 2770 5 %
Rwork0.1333 --
obs0.135 55385 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 30 316 3050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883011
X-RAY DIFFRACTIONf_angle_d0.97624104
X-RAY DIFFRACTIONf_chiral_restr0.0563421
X-RAY DIFFRACTIONf_plane_restr0.0068611
X-RAY DIFFRACTIONf_dihedral_angle_d17.65011824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.3692900.3511720X-RAY DIFFRACTION64.03
1.58-1.610.22721400.17722663X-RAY DIFFRACTION99.29
1.61-1.640.19191430.16132702X-RAY DIFFRACTION98.61
1.64-1.670.20821410.15072670X-RAY DIFFRACTION98.32
1.67-1.710.19031360.15092591X-RAY DIFFRACTION96.67
1.71-1.750.22571410.14812689X-RAY DIFFRACTION98.88
1.75-1.790.21371410.15082662X-RAY DIFFRACTION98.73
1.79-1.840.20091400.13322666X-RAY DIFFRACTION98.73
1.84-1.90.17481400.11962661X-RAY DIFFRACTION98.77
1.9-1.960.15131400.11442668X-RAY DIFFRACTION98.84
1.96-2.030.14921410.11562662X-RAY DIFFRACTION98.7
2.03-2.110.17151410.11652697X-RAY DIFFRACTION98.47
2.11-2.210.16281370.11552596X-RAY DIFFRACTION96.74
2.21-2.320.15261440.11172727X-RAY DIFFRACTION99.58
2.32-2.470.12751410.11422693X-RAY DIFFRACTION99.79
2.47-2.660.15761430.11962711X-RAY DIFFRACTION99.62
2.66-2.920.15391420.13232702X-RAY DIFFRACTION99.27
2.92-3.350.17941400.13172663X-RAY DIFFRACTION97.36
3.35-4.220.15691440.12742723X-RAY DIFFRACTION99.24
4.22-42.960.16831450.16312749X-RAY DIFFRACTION98.27

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