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- PDB-2bbf: Crystal structure of tRNA-guanine transglycosylase (TGT) from Zym... -

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Basic information

Entry
Database: PDB / ID: 2bbf
TitleCrystal structure of tRNA-guanine transglycosylase (TGT) from Zymomonas mobilis in complex with 6-amino-3,7-dihydro-imidazo[4,5-g]quinazolin-8-one
ComponentstRNA guanine transglycosylase
KeywordsTRANSFERASE / protein-ligand complex
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
Chem-344 / : / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsStengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding.
Authors: Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G.
#1: Journal: To be Published
Title: Synthesis, biological evaluation and crystallographic studies of extended guanine-based (lin-benzoguanine) inhibitors for tRNA-guanine transglycosylase (TGT)
Authors: Meyer, E.A. / Donati, N. / Guillot, M. / Schweizer, B. / Diederich, F. / Stengl, B. / Heine, A. / Brenk, R. / Klebe, G.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 19, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details ..._pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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: tRNA guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1923
Polymers42,9261
Non-polymers2672
Water6,648369
1
A: tRNA guanine transglycosylase
hetero molecules

A: tRNA guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3856
Polymers85,8512
Non-polymers5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4180 Å2
ΔGint-4 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.200, 65.590, 69.810
Angle α, β, γ (deg.)90.00, 96.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA guanine transglycosylase / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / TGT


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / Plasmid: PET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 11095422, UniProt: P28720*PLUS, 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-344 / 6-AMINO-3,7-DIHYDRO-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE


Mass: 201.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, MES, DMSO, DTT, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 2002 / Details: MIRRORS
RadiationMonochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 44525 / % possible obs: 98.7 % / Rsym value: 0.043
Reflection shellResolution: 1.7→1.73 Å / Rsym value: 0.0167 / % possible all: 99.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PUD

1pud


Resolution: 1.7→32.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 662304.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4450 10.1 %RANDOM
Rwork0.196 ---
obs0.196 44059 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6745 Å2 / ksol: 0.359238 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.56 Å2
2---1.99 Å20 Å2
3---1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 16 369 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 698 9.7 %
Rwork0.25 6502 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5144.par144.top

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