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- PDB-1ozm: Y106F mutant of Z. mobilis TGT -

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Basic information

Entry
Database: PDB / ID: 1ozm
TitleY106F mutant of Z. mobilis TGT
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 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 1.3Aug 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 / 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 1.4Oct 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 1.5Aug 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)42,9752
Polymers42,9101
Non-polymers651
Water6,179343
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9504
Polymers85,8192
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3270 Å2
ΔGint-14 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.390, 64.720, 71.880
Angle α, β, γ (deg.)90.00, 97.02, 90.00
Int Tables number5
Space group name H-MC121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.3 Å3/Da / Density % sol: 46.02 %
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: May 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: 1.95→40 Å / Num. all: 29077 / Num. obs: 29077 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rsym value: 0.07
Reflection shellResolution: 1.95→2.02 Å / Rsym value: 0.294 / % possible all: 94
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 109129 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.294

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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: 1.95→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 696 -RANDOM
Rwork0.184 ---
all-29077 --
obs-28919 96.4 %-
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 1 343 3245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection
Rfree0.272 18
Rwork0.219 -
obs-2102
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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