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- PDB-5lps: tRNA guanine Transglycosylase (TGT) in co-crystallized complex (s... -

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Basic information

Entry
Database: PDB / ID: 5lps
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2) with 6-amino-2-(methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5,6-tetramethoxytetrahydro-2H-pyran-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-726 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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)43,5164
Polymers42,9261
Non-polymers5903
Water4,522251
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0318
Polymers85,8512
Non-polymers1,1806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3050 Å2
ΔGint-87 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.951, 64.573, 71.001
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number5
Space group name H-MC121

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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)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-726 / 6-azanyl-2-(methylamino)-4-[2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5,6-tetramethoxyoxan-2-yl]ethyl]-1,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 462.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N6O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.27→42.39 Å / Num. obs: 97768 / % possible obs: 96.7 % / Redundancy: 3.8 % / Rsym value: 0.036 / Net I/σ(I): 17.2
Reflection shellResolution: 1.27→1.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4

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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: 1.27→42.37 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 4888 5 %5% random selection
Rwork0.1501 ---
obs0.151 97758 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.27→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 37 251 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052889
X-RAY DIFFRACTIONf_angle_d0.8113927
X-RAY DIFFRACTIONf_dihedral_angle_d20.2861084
X-RAY DIFFRACTIONf_chiral_restr0.071413
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28330.33611470.28112794X-RAY DIFFRACTION89
1.2833-1.29840.29051610.23693058X-RAY DIFFRACTION95
1.2984-1.31430.22691580.21933006X-RAY DIFFRACTION94
1.3143-1.33090.26061600.21283026X-RAY DIFFRACTION95
1.3309-1.34840.2161560.19532971X-RAY DIFFRACTION94
1.3484-1.36690.21691630.18643090X-RAY DIFFRACTION95
1.3669-1.38640.20871580.18032993X-RAY DIFFRACTION95
1.3864-1.40710.20881610.17963073X-RAY DIFFRACTION95
1.4071-1.42910.21791590.18033015X-RAY DIFFRACTION94
1.4291-1.45250.19751600.16443046X-RAY DIFFRACTION96
1.4525-1.47760.17941630.14693099X-RAY DIFFRACTION97
1.4776-1.50440.17331620.13653073X-RAY DIFFRACTION97
1.5044-1.53340.15711650.13133138X-RAY DIFFRACTION97
1.5334-1.56470.15371630.12413083X-RAY DIFFRACTION97
1.5647-1.59870.17331640.12553121X-RAY DIFFRACTION97
1.5987-1.63590.17441630.12313102X-RAY DIFFRACTION98
1.6359-1.67680.14781650.12523130X-RAY DIFFRACTION98
1.6768-1.72210.16111640.12393124X-RAY DIFFRACTION97
1.7221-1.77280.13811630.12493096X-RAY DIFFRACTION96
1.7728-1.830.17191630.12983094X-RAY DIFFRACTION98
1.83-1.89540.16611660.13333156X-RAY DIFFRACTION98
1.8954-1.97130.16161670.13053166X-RAY DIFFRACTION98
1.9713-2.0610.1531650.13313146X-RAY DIFFRACTION99
2.061-2.16970.16271660.13463147X-RAY DIFFRACTION98
2.1697-2.30560.16681670.14273168X-RAY DIFFRACTION99
2.3056-2.48360.1521640.14973111X-RAY DIFFRACTION97
2.4836-2.73350.16681680.1563207X-RAY DIFFRACTION99
2.7335-3.1290.17131690.15323208X-RAY DIFFRACTION99
3.129-3.94170.14951690.1493213X-RAY DIFFRACTION99
3.9417-42.370.17461690.16923216X-RAY DIFFRACTION97

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