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- PDB-1ozq: CRYSTAL STRUCTURE OF THE MUTATED TRNA-GUANINE TRANSGLYCOSYLASE (T... -

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Basic information

Entry
Database: PDB / ID: 1ozq
TitleCRYSTAL STRUCTURE OF THE MUTATED TRNA-GUANINE TRANSGLYCOSYLASE (TGT)Y106F COMPLEXED WITH PREQ1
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / mutated protein (Y106F)
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
7-DEAZA-7-AMINOMETHYL-GUANINE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBrenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Chembiochem / Year: 2003
Title: Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design
Authors: Brenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / Klebe, G.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _struct_conn.ptnr1_auth_comp_id ..._pdbx_struct_assembly_prop.biol_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,1543
Polymers42,9101
Non-polymers2452
Water6,575365
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3096
Polymers85,8192
Non-polymers4894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4150 Å2
ΔGint-10 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.250, 65.020, 71.400
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1262-

HOH

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Components

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


Mass: 42909.703 Da / Num. of mol.: 1 / Mutation: Y106F
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: 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-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.26 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, DMSO, DTT , pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoir
213 %PEG80001reservoir
31 mMdithiothreitol1reservoir
40.2 %agarose1reservoir
510 mMHEPES1droppH7.5
62 M1dropNaCl
71 mMdithiothreitol1drop
812 mg/mlprotein1drop

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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: Apr 28, 2001 / 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: 1.9→40 Å / Num. all: 31900 / Num. obs: 31900 / % possible obs: 98.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.064
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.274 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 98882 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.274

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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: 1.9→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1635766 / Data cutoff high rms absF: 1635766 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3191 10 %RANDOM
Rwork0.178 ---
obs0.178 31889 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2684 Å2 / ksol: 0.329622 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-1.65 Å2
2---3.25 Å20 Å2
3----0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 14 365 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 519 10 %
Rwork0.215 4652 -
obs--96.2 %
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 DIFFRACTION5PQ1.PARPQ1.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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