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- PDB-6yh3: tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 6yh3
TitletRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-(methylamino)-4-phenethyl-1,7-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-OQN / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization, 19F NMR and nanoESI-MS 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)43,5423
Polymers43,1421
Non-polymers4002
Water5,405300
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0836
Polymers86,2842
Non-polymers8004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2110 Å2
ΔGint-14 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.934, 65.196, 71.597
Angle α, β, γ (deg.)90.000, 94.218, 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-OQN / 6-amino-2-(methylamino)-4-phenethyl-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 6-azanyl-2-(methylamino)-4-(2-phenylethyl)-3,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 334.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
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: Sep 4, 2017
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: 1.49→42.78 Å / Num. obs: 61850 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.18
Reflection shellResolution: 1.49→1.58 Å / Num. unique obs: 9665 / CC1/2: 0.852

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Processing

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

1pud


Resolution: 1.49→42.78 Å / SU ML: 0.1621 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1646 3091 5 %
Rwork0.1338 58741 -
obs0.1353 61832 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.84 Å2
Refinement stepCycle: LAST / Resolution: 1.49→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 26 300 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742874
X-RAY DIFFRACTIONf_angle_d0.93953902
X-RAY DIFFRACTIONf_chiral_restr0.0679405
X-RAY DIFFRACTIONf_plane_restr0.0064554
X-RAY DIFFRACTIONf_dihedral_angle_d23.24581056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.3381310.31122491X-RAY DIFFRACTION92.62
1.51-1.540.29621370.24192602X-RAY DIFFRACTION95.84
1.54-1.570.22651370.18752589X-RAY DIFFRACTION94.26
1.57-1.590.21381380.15132640X-RAY DIFFRACTION96.96
1.59-1.620.19691420.14082704X-RAY DIFFRACTION97.73
1.62-1.660.20331390.13122633X-RAY DIFFRACTION97.85
1.66-1.690.17241420.13262690X-RAY DIFFRACTION97.82
1.69-1.730.17731400.13182688X-RAY DIFFRACTION97.72
1.73-1.780.15931400.11932656X-RAY DIFFRACTION97.86
1.78-1.820.1671380.11392627X-RAY DIFFRACTION97.36
1.82-1.880.14521380.11112624X-RAY DIFFRACTION95.34
1.88-1.940.13741430.11262709X-RAY DIFFRACTION98.41
1.94-2.010.141400.10772658X-RAY DIFFRACTION97.93
2.01-2.090.13471420.11322711X-RAY DIFFRACTION98.38
2.09-2.180.15091420.1112691X-RAY DIFFRACTION98.3
2.18-2.30.16711430.11642708X-RAY DIFFRACTION98.62
2.3-2.440.14711380.11712639X-RAY DIFFRACTION96.02
2.44-2.630.14281440.11992729X-RAY DIFFRACTION99.17
2.63-2.90.15021430.1322723X-RAY DIFFRACTION99.24
2.9-3.320.13911450.13872745X-RAY DIFFRACTION98.94
3.32-4.180.18971420.13272703X-RAY DIFFRACTION97.57
4.18-42.780.17811470.1612781X-RAY DIFFRACTION98.35

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