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- PDB-5i09: tRNA guanine transglycosylase (TGT) in soaked complex with Furano... -

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Basic information

Entry
Database: PDB / ID: 5i09
TitletRNA guanine transglycosylase (TGT) in soaked complex with Furanoside-Based lin-Benzoguanine 3
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / soaking / shigellosis / TRANSFERASE INHIBITOR
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
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-1UD / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors
Authors: Ehrmann, F.R. / Stojo, J. / Heine, A. / Diederich, F. / Reuter, K. / Sanglier-Cianferani, S. / Klebe, G.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,6726
Polymers42,9261
Non-polymers7465
Water6,990388
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,34412
Polymers85,8512
Non-polymers1,49210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4560 Å2
ΔGint-23 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.989, 65.091, 70.776
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-854-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1UD / methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-3-O-methyl-beta-D-ribo-hexofuranoside


Mass: 404.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 49.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.44→45.22 Å / Num. obs: 74015 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rsym value: 0.051 / Net I/σ(I): 14.9
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1492refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.44→23.449 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.23
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 3698 5 %random selection
Rwork0.1329 ---
obs0.1346 73978 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.44→23.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 45 388 3232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053099
X-RAY DIFFRACTIONf_angle_d0.7874203
X-RAY DIFFRACTIONf_dihedral_angle_d21.4881169
X-RAY DIFFRACTIONf_chiral_restr0.068441
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4393-1.45830.23981370.19992600X-RAY DIFFRACTION97
1.4583-1.47820.2671440.19182749X-RAY DIFFRACTION100
1.4782-1.49940.18491410.17862664X-RAY DIFFRACTION100
1.4994-1.52170.20271410.16642692X-RAY DIFFRACTION100
1.5217-1.54550.22751430.16082716X-RAY DIFFRACTION100
1.5455-1.57080.191410.15572682X-RAY DIFFRACTION100
1.5708-1.59790.19081460.13832764X-RAY DIFFRACTION100
1.5979-1.6270.17071400.1352658X-RAY DIFFRACTION100
1.627-1.65830.16881420.12922711X-RAY DIFFRACTION100
1.6583-1.69210.21430.12472704X-RAY DIFFRACTION100
1.6921-1.72890.16141410.12122684X-RAY DIFFRACTION100
1.7289-1.76910.13881420.11512694X-RAY DIFFRACTION100
1.7691-1.81330.15851430.11822725X-RAY DIFFRACTION100
1.8133-1.86230.17221430.11772707X-RAY DIFFRACTION100
1.8623-1.91710.15091430.11792723X-RAY DIFFRACTION100
1.9171-1.97890.16971400.11752668X-RAY DIFFRACTION100
1.9789-2.04960.14061430.11672717X-RAY DIFFRACTION100
2.0496-2.13160.15451420.11922700X-RAY DIFFRACTION100
2.1316-2.22860.15031440.122732X-RAY DIFFRACTION100
2.2286-2.3460.14271430.11922711X-RAY DIFFRACTION100
2.346-2.49280.18751420.13142695X-RAY DIFFRACTION100
2.4928-2.6850.17151440.13572742X-RAY DIFFRACTION100
2.685-2.95480.16941430.13412708X-RAY DIFFRACTION100
2.9548-3.38120.16491420.13452710X-RAY DIFFRACTION100
3.3812-4.25580.14611440.12612731X-RAY DIFFRACTION99
4.2558-23.45250.17151410.15362693X-RAY DIFFRACTION96

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