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- PDB-6ygy: tRNA-Guanine Transglycosylase (TGT) labeled with 5-fluorotryptoph... -

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Basic information

Entry
Database: PDB / ID: 6ygy
TitletRNA-Guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-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 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-NEZ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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)43,5273
Polymers43,1421
Non-polymers3852
Water5,423301
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0536
Polymers86,2842
Non-polymers7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3620 Å2
ΔGint-23 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.224, 65.050, 71.561
Angle α, β, γ (deg.)90.000, 94.280, 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 (strain ATCC 31821 / ZM4 / CP4) (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-NEZ / 6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE


Mass: 319.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 46.35 %
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: 1.52→37.77 Å / Num. obs: 58507 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.43 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.42
Reflection shellResolution: 1.52→1.61 Å / Num. unique obs: 9042 / CC1/2: 0.836

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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: 1.52→37.77 Å / SU ML: 0.1551 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.7897
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1823 2926 5 %
Rwork0.1454 55573 -
obs0.1472 58499 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 1.52→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 25 301 3011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822860
X-RAY DIFFRACTIONf_angle_d1.00133881
X-RAY DIFFRACTIONf_chiral_restr0.0524404
X-RAY DIFFRACTIONf_plane_restr0.0066549
X-RAY DIFFRACTIONf_dihedral_angle_d13.58031714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.28511290.22882440X-RAY DIFFRACTION89.2
1.54-1.570.25351270.20212427X-RAY DIFFRACTION90.5
1.57-1.60.23341390.17022639X-RAY DIFFRACTION96.96
1.6-1.630.2211410.15662674X-RAY DIFFRACTION97.51
1.63-1.660.22611380.15112624X-RAY DIFFRACTION97.53
1.66-1.70.21391410.14542664X-RAY DIFFRACTION97.53
1.7-1.740.19861400.14912666X-RAY DIFFRACTION97.91
1.74-1.780.18411400.14362660X-RAY DIFFRACTION97.8
1.78-1.830.20561400.13382657X-RAY DIFFRACTION97.83
1.83-1.880.18051390.13192648X-RAY DIFFRACTION98.13
1.88-1.940.18681400.1342655X-RAY DIFFRACTION97.8
1.94-2.010.1941410.12962674X-RAY DIFFRACTION97.84
2.01-2.090.16211400.13322675X-RAY DIFFRACTION97.54
2.09-2.190.18071320.12792492X-RAY DIFFRACTION92.3
2.19-2.30.17051420.12992715X-RAY DIFFRACTION99.06
2.3-2.450.17791430.13482709X-RAY DIFFRACTION99.23
2.45-2.640.17231430.13932721X-RAY DIFFRACTION99.34
2.64-2.90.17461420.14242698X-RAY DIFFRACTION99.2
2.9-3.320.17241440.14812739X-RAY DIFFRACTION99.21
3.32-4.190.1661380.14242614X-RAY DIFFRACTION94.7
4.19-37.770.19041470.16562782X-RAY DIFFRACTION99.02

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