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

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Basic information

Entry
Database: PDB / ID: 6fpu
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3aS,5aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis([1,3]dioxolo)[4,5-b:4',5'-d]pyran-3a-yl)methyl)amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / CO-CRYSTALLIZATION / 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-E48 / 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 12, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)43,6696
Polymers42,9261
Non-polymers7445
Water6,720373
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33812
Polymers85,8512
Non-polymers1,48710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4780 Å2
ΔGint-39 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.623, 64.690, 70.502
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-828-

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)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 378 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-E48 / 6-azanyl-2-[[(1~{R},2~{S},6~{S},9~{R})-4,4,11,11-tetramethyl-3,5,7,10,12-pentaoxatricyclo[7.3.0.0^{2,6}]dodecan-6-yl]methylamino]-3,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 458.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 47.7 %
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: 1.36→44.23 Å / Num. obs: 83230 / % possible obs: 96.8 % / Redundancy: 3.6 % / Rrim(I) all: 0.053 / Rsym value: 0.045 / Net I/σ(I): 14.3
Reflection shellResolution: 1.36→1.44 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12915 / Rrim(I) all: 0.586 / Rsym value: 0.496 / % possible all: 93

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Processing

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

1pud


Resolution: 1.36→44.229 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.77
RfactorNum. reflection% reflection
Rfree0.1542 4158 5 %
Rwork0.128 --
obs0.1293 83197 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→44.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 44 373 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073063
X-RAY DIFFRACTIONf_angle_d0.9474157
X-RAY DIFFRACTIONf_dihedral_angle_d22.1871160
X-RAY DIFFRACTIONf_chiral_restr0.069436
X-RAY DIFFRACTIONf_plane_restr0.007577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3720.2671040.25711996X-RAY DIFFRACTION73
1.372-1.38810.29481370.23022616X-RAY DIFFRACTION97
1.3881-1.40510.19891430.19652710X-RAY DIFFRACTION99
1.4051-1.42280.24471380.18292611X-RAY DIFFRACTION99
1.4228-1.44160.25011410.17882698X-RAY DIFFRACTION99
1.4416-1.46130.20631380.17032622X-RAY DIFFRACTION99
1.4613-1.48220.19641410.15972693X-RAY DIFFRACTION98
1.4822-1.50430.18811410.15052682X-RAY DIFFRACTION98
1.5043-1.52780.20521380.15682614X-RAY DIFFRACTION97
1.5278-1.55290.17811380.14092629X-RAY DIFFRACTION98
1.5529-1.57960.20511390.13362647X-RAY DIFFRACTION97
1.5796-1.60840.17281350.13692569X-RAY DIFFRACTION95
1.6084-1.63930.17551400.12552656X-RAY DIFFRACTION97
1.6393-1.67280.14411420.11392697X-RAY DIFFRACTION100
1.6728-1.70910.16171420.11432691X-RAY DIFFRACTION98
1.7091-1.74890.12961400.11042668X-RAY DIFFRACTION99
1.7489-1.79260.13741390.10632636X-RAY DIFFRACTION98
1.7926-1.84110.14451420.11042691X-RAY DIFFRACTION99
1.8411-1.89530.15031400.11832661X-RAY DIFFRACTION97
1.8953-1.95650.16441370.11752602X-RAY DIFFRACTION95
1.9565-2.02640.14161360.11452581X-RAY DIFFRACTION95
2.0264-2.10750.15551340.11412556X-RAY DIFFRACTION95
2.1075-2.20340.1511430.11192713X-RAY DIFFRACTION99
2.2034-2.31960.1361400.11072671X-RAY DIFFRACTION98
2.3196-2.46490.13811430.11512714X-RAY DIFFRACTION99
2.4649-2.65520.13781400.11782664X-RAY DIFFRACTION98
2.6552-2.92240.14941370.11792590X-RAY DIFFRACTION95
2.9224-3.34510.13661430.12812718X-RAY DIFFRACTION98
3.3451-4.2140.14631420.12672702X-RAY DIFFRACTION98
4.214-44.25270.14991450.14472741X-RAY DIFFRACTION97

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