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- PDB-5lpo: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5lpo
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Carbohydrate-based Inhibitors / homodimer / 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-725 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Carbohydrate-based Inhibitors targeting the Ribose-34 pocket of Z.mobilis TGT and changing the oligomeric state of the homodimer
Authors: Ehrmann, F.R. / Botzanowski, T. / Pfaffender, T. / Heine, A. / Diederich, F. / Sanglier-Cianferani, S. / Klebe, G.
History
DepositionAug 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
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: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,27010
Polymers43,0701
Non-polymers1,2019
Water5,062281
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,54120
Polymers86,1402
Non-polymers2,40118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6130 Å2
ΔGint-11 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.662, 64.819, 71.241
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43069.828 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)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 290 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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: Chemical ChemComp-725 / 6-amino-2-(methylamino)-4-(2-((2R,3R,4R,5R)-3,4,5-trimethoxytetrahydrofuran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one


Mass: 418.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N6O5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
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: 14.1 / Wavelength: 0.918408 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918408 Å / Relative weight: 1
ReflectionResolution: 1.42→42.44 Å / Num. obs: 71176 / % possible obs: 97.8 % / Redundancy: 3 % / Rsym value: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.9 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 1492)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.42→42.44 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.68
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 3559 5 %5% random selection
Rwork0.132 ---
obs0.1335 71169 97.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 77 281 3098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053105
X-RAY DIFFRACTIONf_angle_d0.8264208
X-RAY DIFFRACTIONf_dihedral_angle_d19.7521166
X-RAY DIFFRACTIONf_chiral_restr0.071440
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.43770.29681110.24572121X-RAY DIFFRACTION76
1.4377-1.45830.24961240.20242351X-RAY DIFFRACTION87
1.4583-1.48010.21791430.17322713X-RAY DIFFRACTION97
1.4801-1.50320.1941430.1432721X-RAY DIFFRACTION100
1.5032-1.52780.20661450.13922742X-RAY DIFFRACTION99
1.5278-1.55420.18981440.12872744X-RAY DIFFRACTION100
1.5542-1.58240.15051460.12142774X-RAY DIFFRACTION100
1.5824-1.61290.18481440.11562726X-RAY DIFFRACTION100
1.6129-1.64580.15671430.11452728X-RAY DIFFRACTION100
1.6458-1.68160.14481460.11452765X-RAY DIFFRACTION100
1.6816-1.72070.15711460.11782772X-RAY DIFFRACTION100
1.7207-1.76370.15631430.11252726X-RAY DIFFRACTION100
1.7637-1.81140.1541440.11052740X-RAY DIFFRACTION100
1.8114-1.86470.151450.11292759X-RAY DIFFRACTION100
1.8647-1.92490.17251450.11432737X-RAY DIFFRACTION99
1.9249-1.99370.15821420.11492711X-RAY DIFFRACTION99
1.9937-2.07350.14331450.11632743X-RAY DIFFRACTION99
2.0735-2.16790.16481440.11582753X-RAY DIFFRACTION100
2.1679-2.28220.17051450.1272745X-RAY DIFFRACTION99
2.2822-2.42520.14361460.12862764X-RAY DIFFRACTION100
2.4252-2.61240.17321430.13762735X-RAY DIFFRACTION99
2.6124-2.87520.16371440.13632737X-RAY DIFFRACTION99
2.8752-3.29110.16521460.13952767X-RAY DIFFRACTION99
3.2911-4.14590.13771450.12922747X-RAY DIFFRACTION98
4.1459-42.440.1681470.15452789X-RAY DIFFRACTION98

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