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

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Basic information

Entry
Database: PDB / ID: 5lpp
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group C2) with 6-amino-4-(2-((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)ethyl)-2-(methylamino)-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-guanine transglycosylation / queuosine 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-72C / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)43,4223
Polymers42,9261
Non-polymers4962
Water2,774154
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8436
Polymers85,8512
Non-polymers9924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2530 Å2
ΔGint-22 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.423, 64.443, 71.223
Angle α, β, γ (deg.)90.00, 93.88, 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)
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-72C / 4-[2-[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-methoxy-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]ethyl]-6-azanyl-2-(methylamino)-1,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 430.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 45.9 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→42.61 Å / Num. obs: 26417 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rsym value: 0.054 / Net I/σ(I): 15.8
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3

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Processing

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

1p0d


Resolution: 1.99→42.61 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1321 5 %5% random selection
Rwork0.1807 ---
obs0.1825 26415 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 28 154 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072693
X-RAY DIFFRACTIONf_angle_d0.7993637
X-RAY DIFFRACTIONf_dihedral_angle_d17.2151613
X-RAY DIFFRACTIONf_chiral_restr0.049385
X-RAY DIFFRACTIONf_plane_restr0.006503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.07010.3151450.24672757X-RAY DIFFRACTION99
2.0701-2.16430.23361460.20042776X-RAY DIFFRACTION99
2.1643-2.27840.22271460.19752780X-RAY DIFFRACTION100
2.2784-2.42110.25131460.18242776X-RAY DIFFRACTION100
2.4211-2.6080.27861460.19182772X-RAY DIFFRACTION99
2.608-2.87040.26251460.19342773X-RAY DIFFRACTION99
2.8704-3.28570.19941470.17732787X-RAY DIFFRACTION100
3.2857-4.13910.18191480.15972823X-RAY DIFFRACTION100
4.1391-42.610.19671510.1772850X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3224-0.5926-0.0794-0.04560.30411.08050.0223-0.024-0.15360.0344-0.03740.044-0.0336-0.1012-0.00010.24560.031-0.01170.22740.01680.285394.07524.134920.1343
21.32120.3531-0.12310.1781-0.21730.53420.0188-0.4837-0.109-0.441-0.3174-0.6445-0.04140.11370.0130.56850.0730.00990.3122-0.07410.375294.01725.743330.7228
30.124-0.07710.10550.095-0.00420.25940.0312-0.17360.1416-0.0160.0237-0.0373-0.17210.0803-00.3020.03240.01610.3305-0.02230.273292.624713.882429.5093
41.6108-0.3739-0.49451.43150.39341.27870.0674-0.26710.19320.03020.0624-0.1208-0.32750.16650.00060.2875-0.0098-0.00380.2533-0.03410.255106.863813.266325.4684
50.4891-0.46841.2469-0.0987-0.74430.86550.06440.1073-0.0486-0.1137-0.02570.01270.12080.15820.00010.28250.01120.00460.31070.01820.2949102.36687.2739-2.3736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:105)
2X-RAY DIFFRACTION2(chain A and resid 106:135)
3X-RAY DIFFRACTION3(chain A and resid 136:159)
4X-RAY DIFFRACTION4(chain A and resid 160:289)
5X-RAY DIFFRACTION5(chain A and resid 290:382)

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