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

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Basic information

Entry
Database: PDB / ID: 5lpq
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group P21) 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 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-72C / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
B: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8436
Polymers85,8512
Non-polymers9924
Water1,892105
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-18 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 78.851, 84.943
Angle α, β, γ (deg.)90.00, 109.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42925.703 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C20H26N6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 2.52→50.09 Å / Num. obs: 28457 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rsym value: 0.114 / Net I/σ(I): 9.9
Reflection shellResolution: 2.52→2.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.479 / 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: 2.52→43.67 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1423 5 %5% random selection
Rwork0.2271 ---
obs0.2289 28448 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.52→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5441 0 64 105 5610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045639
X-RAY DIFFRACTIONf_angle_d0.4797622
X-RAY DIFFRACTIONf_dihedral_angle_d17.0533368
X-RAY DIFFRACTIONf_chiral_restr0.037813
X-RAY DIFFRACTIONf_plane_restr0.0041050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.61260.33231210.30512305X-RAY DIFFRACTION84
2.6126-2.71720.3171440.26732742X-RAY DIFFRACTION100
2.7172-2.84080.30021440.27562736X-RAY DIFFRACTION99
2.8408-2.99060.3011440.26852730X-RAY DIFFRACTION100
2.9906-3.17790.31441430.26082721X-RAY DIFFRACTION100
3.1779-3.42320.27331450.24032753X-RAY DIFFRACTION100
3.4232-3.76750.25941430.22442718X-RAY DIFFRACTION100
3.7675-4.31230.20291440.19692737X-RAY DIFFRACTION99
4.3123-5.43140.24161460.18522766X-RAY DIFFRACTION100
5.4314-43.670.23661490.20242817X-RAY DIFFRACTION99

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