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- PDB-6fmn: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 6fmn
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)methyl)amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / CO-CRYSTALLIZATION / CARBOHYDRATES / 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-E4E / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: Chemistry / Year: 2018
Title: Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase.
Authors: Movsisyan, L.D. / Schafer, E. / Nguyen, A. / Ehrmann, F.R. / Schwab, A. / Rossolini, T. / Zimmerli, D. / Wagner, B. / Daff, H. / Heine, A. / Klebe, G. / Diederich, F.
History
DepositionFeb 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)43,6657
Polymers42,9261
Non-polymers7396
Water7,476415
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33014
Polymers85,8512
Non-polymers1,47912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5260 Å2
ΔGint-39 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.672, 64.267, 70.690
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

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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: 42925.703 Da / Num. of mol.: 1 / Mutation: T312K
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 , 5 types, 421 molecules

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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-E4E / 6-azanyl-2-[[(2~{R},3~{S},4~{R},5~{R})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-3,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 362.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H18N6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100MM MES, 10%, DMSO, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.34→44.77 Å / Num. obs: 86836 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rrim(I) all: 0.097 / Rsym value: 0.081 / Net I/σ(I): 9
Reflection shellResolution: 1.34→1.42 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 13420 / Rrim(I) all: 0.539 / Rsym value: 0.446 / % possible all: 93.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.36→44.768 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.18
RfactorNum. reflection% reflection
Rfree0.1554 4196 5 %
Rwork0.1222 --
obs0.1239 83933 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→44.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 45 415 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073124
X-RAY DIFFRACTIONf_angle_d0.954234
X-RAY DIFFRACTIONf_dihedral_angle_d21.1211181
X-RAY DIFFRACTIONf_chiral_restr0.07443
X-RAY DIFFRACTIONf_plane_restr0.007591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.37550.28191380.2562618X-RAY DIFFRACTION97
1.3755-1.39160.31581350.24342577X-RAY DIFFRACTION96
1.3916-1.40860.23891420.19682699X-RAY DIFFRACTION99
1.4086-1.42640.18821410.1562667X-RAY DIFFRACTION99
1.4264-1.44520.18831400.14532674X-RAY DIFFRACTION99
1.4452-1.4650.17751420.13532694X-RAY DIFFRACTION99
1.465-1.48590.18811410.13442681X-RAY DIFFRACTION98
1.4859-1.50810.16991390.1312629X-RAY DIFFRACTION99
1.5081-1.53170.17771410.13182683X-RAY DIFFRACTION98
1.5317-1.55680.14641400.11412658X-RAY DIFFRACTION99
1.5568-1.58370.13631400.10332673X-RAY DIFFRACTION98
1.5837-1.61250.13861410.10312671X-RAY DIFFRACTION98
1.6125-1.64350.17171390.10182639X-RAY DIFFRACTION98
1.6435-1.6770.13581410.10892672X-RAY DIFFRACTION98
1.677-1.71350.15281350.11372568X-RAY DIFFRACTION95
1.7135-1.75330.16471390.10982647X-RAY DIFFRACTION97
1.7533-1.79720.16491400.10642668X-RAY DIFFRACTION99
1.7972-1.84580.13591420.10672690X-RAY DIFFRACTION98
1.8458-1.90010.14871420.1062704X-RAY DIFFRACTION98
1.9001-1.96140.14381400.11032645X-RAY DIFFRACTION98
1.9614-2.03150.13871400.11172670X-RAY DIFFRACTION98
2.0315-2.11290.14171390.11252633X-RAY DIFFRACTION97
2.1129-2.2090.14671380.11112628X-RAY DIFFRACTION96
2.209-2.32550.13391360.10952590X-RAY DIFFRACTION96
2.3255-2.47120.13461350.11592553X-RAY DIFFRACTION93
2.4712-2.6620.14741420.11762695X-RAY DIFFRACTION99
2.662-2.92980.16341430.11632718X-RAY DIFFRACTION99
2.9298-3.35360.17291410.12312685X-RAY DIFFRACTION99
3.3536-4.22470.15121400.12032662X-RAY DIFFRACTION96
4.2247-44.79250.14231440.14382746X-RAY DIFFRACTION97

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