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- PDB-4gd0: tRNA-guanine transglycosylase Y106F, C158V mutant -

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Basic information

Entry
Database: PDB / ID: 4gd0
TitletRNA-guanine transglycosylase Y106F, C158V mutant
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / substrate specificity / bacterial TGT / preQ1 / tRNA / guanine exchange enzyme
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsSchmidt, I. / Tidten-Luksch, N. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Plos One / Year: 2013
Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor.
Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,4327
Polymers42,9061
Non-polymers5266
Water9,440524
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,86314
Polymers85,8112
Non-polymers1,05212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5760 Å2
ΔGint-61 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.428, 64.986, 70.203
Angle α, β, γ (deg.)90.00, 96.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21A-696-

HOH

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Components

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


Mass: 42905.691 Da / Num. of mol.: 1 / Mutation: Y106F, C158V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM-Y106F_C158V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE(3) pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR 312 TO LYS CONFLICT IN UNP ENTRY P28720

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 1 mM DTT, 10 % DMSO, 12% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2010 / Details: morror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. all: 99752 / Num. obs: 99752 / % possible obs: 97.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 8.85 Å2 / Net I/σ(I): 22.1
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.02 / Num. unique all: 4187 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GEV

3gev
PDB Unreleased entry


Resolution: 1.29→16.275 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / Cross valid method: R_free / σ(F): 1 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 9637 10.02 %Random, 10%
Rwork0.1628 ---
obs0.1651 96177 93.7 %-
all-96177 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.833 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0306 Å2-0 Å21.7146 Å2
2---1.1613 Å2-0 Å2
3---1.1919 Å2
Refinement stepCycle: LAST / Resolution: 1.29→16.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 31 524 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053091
X-RAY DIFFRACTIONf_angle_d1.064199
X-RAY DIFFRACTIONf_dihedral_angle_d12.4161178
X-RAY DIFFRACTIONf_chiral_restr0.069447
X-RAY DIFFRACTIONf_plane_restr0.005560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30470.26572600.22792231X-RAY DIFFRACTION72
1.3047-1.32010.27052380.22212451X-RAY DIFFRACTION79
1.3201-1.33620.22333040.20192556X-RAY DIFFRACTION84
1.3362-1.35310.24072850.18972661X-RAY DIFFRACTION87
1.3531-1.37090.21762990.18722718X-RAY DIFFRACTION88
1.3709-1.38960.22092900.1812736X-RAY DIFFRACTION90
1.3896-1.40950.21863180.17842876X-RAY DIFFRACTION92
1.4095-1.43050.21933020.16822784X-RAY DIFFRACTION92
1.4305-1.45280.20922940.16582869X-RAY DIFFRACTION93
1.4528-1.47660.19293310.16042916X-RAY DIFFRACTION94
1.4766-1.50210.23180.15332855X-RAY DIFFRACTION95
1.5021-1.52940.18373210.15312904X-RAY DIFFRACTION95
1.5294-1.55880.17453270.15062957X-RAY DIFFRACTION95
1.5588-1.59060.18713750.15142860X-RAY DIFFRACTION95
1.5906-1.62510.19153360.14992914X-RAY DIFFRACTION96
1.6251-1.66290.18323480.15642908X-RAY DIFFRACTION96
1.6629-1.70440.19853120.16023006X-RAY DIFFRACTION96
1.7044-1.75050.18793350.15832962X-RAY DIFFRACTION97
1.7505-1.80190.19713470.16052977X-RAY DIFFRACTION97
1.8019-1.860.17953220.1543010X-RAY DIFFRACTION98
1.86-1.92640.18753310.16283023X-RAY DIFFRACTION98
1.9264-2.00340.19313380.15933052X-RAY DIFFRACTION99
2.0034-2.09430.17113480.15883057X-RAY DIFFRACTION100
2.0943-2.20450.17713490.15473061X-RAY DIFFRACTION100
2.2045-2.34230.17213740.15723072X-RAY DIFFRACTION99
2.3423-2.52250.18523590.15593022X-RAY DIFFRACTION99
2.5225-2.77520.18363210.16883095X-RAY DIFFRACTION99
2.7752-3.17420.16353180.15723102X-RAY DIFFRACTION99
3.1742-3.98940.16273360.14843047X-RAY DIFFRACTION98
3.9894-16.2750.18713010.18262858X-RAY DIFFRACTION90

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