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- PDB-5jgm: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5jgm
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with ethyl (2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl)carbamate
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / co-crystallization / shigellosis / Prodrugs / 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-810 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsEhrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Carbamate-protected lin-Benzoguanines as promising candidates for improving solubility and membrane permeability
Authors: Ehrmann, F.R. / Hohn, C. / Heine, A. / Reuter, K. / Diederich, F. / Klebe, G.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,79110
Polymers42,9261
Non-polymers8669
Water7,800433
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,58320
Polymers85,8512
Non-polymers1,73118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6500 Å2
ΔGint-21 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.182, 65.407, 71.064
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21A-890-

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
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 , 6 types, 442 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-810 / ethyl [2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl]carbamate


Mass: 302.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N6O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.38→45.29 Å / Num. obs: 84560 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rsym value: 0.041 / Net I/σ(I): 17
Reflection shellResolution: 1.38→1.46 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4

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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: 1.38→43.85 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.46
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 4228 5 %random selection
Rwork0.1339 ---
obs0.1353 84557 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.38→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 54 433 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053111
X-RAY DIFFRACTIONf_angle_d0.7874196
X-RAY DIFFRACTIONf_dihedral_angle_d23.1091180
X-RAY DIFFRACTIONf_chiral_restr0.07436
X-RAY DIFFRACTIONf_plane_restr0.005583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.39440.23621330.23382527X-RAY DIFFRACTION93
1.3944-1.41080.29331370.2252613X-RAY DIFFRACTION99
1.4108-1.4280.26561380.22832630X-RAY DIFFRACTION98
1.428-1.4460.22671420.21312684X-RAY DIFFRACTION99
1.446-1.46510.21381400.18082662X-RAY DIFFRACTION99
1.4651-1.48510.24231400.17062663X-RAY DIFFRACTION98
1.4851-1.50640.1771400.15852661X-RAY DIFFRACTION99
1.5064-1.52880.18531380.15192613X-RAY DIFFRACTION98
1.5288-1.55270.17461410.14032695X-RAY DIFFRACTION99
1.5527-1.57820.20281400.13222659X-RAY DIFFRACTION99
1.5782-1.60540.15781420.12362696X-RAY DIFFRACTION99
1.6054-1.63460.16371400.1242659X-RAY DIFFRACTION99
1.6346-1.6660.15931410.12032674X-RAY DIFFRACTION99
1.666-1.70.15611420.11742692X-RAY DIFFRACTION99
1.7-1.7370.1661400.11472659X-RAY DIFFRACTION100
1.737-1.77740.15781410.12112694X-RAY DIFFRACTION100
1.7774-1.82190.1481420.11572698X-RAY DIFFRACTION100
1.8219-1.87110.16481430.11852705X-RAY DIFFRACTION100
1.8711-1.92620.16021400.12372668X-RAY DIFFRACTION99
1.9262-1.98840.15161400.11872654X-RAY DIFFRACTION100
1.9884-2.05940.15471420.11822704X-RAY DIFFRACTION100
2.0594-2.14190.14851420.11672704X-RAY DIFFRACTION100
2.1419-2.23940.17671440.12922719X-RAY DIFFRACTION100
2.2394-2.35740.16261400.12952673X-RAY DIFFRACTION99
2.3574-2.50510.14581420.1252699X-RAY DIFFRACTION100
2.5051-2.69850.14191440.13512731X-RAY DIFFRACTION100
2.6985-2.970.17741420.13542697X-RAY DIFFRACTION99
2.97-3.39960.13181430.13372715X-RAY DIFFRACTION100
3.3996-4.28260.14991430.12332720X-RAY DIFFRACTION99
4.2826-43.850.16151460.14922761X-RAY DIFFRACTION99

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