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

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Basic information

Entry
Database: PDB / ID: 5jgo
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with allyl (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-6JX / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsEhrmann, F.R. / 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)43,6147
Polymers42,9261
Non-polymers6886
Water6,557364
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,22714
Polymers85,8512
Non-polymers1,37612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5280 Å2
ΔGint-2 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.888, 65.134, 70.835
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-837-

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 , 5 types, 370 molecules

#2: Chemical ChemComp-6JX / allyl (2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-6-yl)carbamate


Mass: 314.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N6O3
#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-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
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: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.37→45.59 Å / Num. obs: 84027 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rsym value: 0.061 / Net I/σ(I): 11.15
Reflection shellResolution: 1.37→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.11 / % possible all: 90.6

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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: 1.37→43.62 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.7
RfactorNum. reflection% reflectionSelection details
Rfree0.1619 4202 5 %random selection
Rwork0.1345 ---
obs0.1358 84018 97.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.37→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 44 364 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053112
X-RAY DIFFRACTIONf_angle_d0.8074209
X-RAY DIFFRACTIONf_dihedral_angle_d21.8511180
X-RAY DIFFRACTIONf_chiral_restr0.073437
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.38620.3868800.31441518X-RAY DIFFRACTION56
1.3862-1.40250.27351430.23812714X-RAY DIFFRACTION99
1.4025-1.41960.21761430.20892705X-RAY DIFFRACTION99
1.4196-1.43760.22261410.20622680X-RAY DIFFRACTION100
1.4376-1.45650.22311410.20122695X-RAY DIFFRACTION100
1.4565-1.47640.2331450.19592737X-RAY DIFFRACTION100
1.4764-1.49750.23041400.18092676X-RAY DIFFRACTION99
1.4975-1.51990.20961420.17142694X-RAY DIFFRACTION99
1.5199-1.54360.19771440.15162736X-RAY DIFFRACTION99
1.5436-1.56890.18391410.13992666X-RAY DIFFRACTION99
1.5689-1.5960.14521430.12432732X-RAY DIFFRACTION100
1.596-1.6250.17691420.11992693X-RAY DIFFRACTION100
1.625-1.65630.16021420.11372704X-RAY DIFFRACTION100
1.6563-1.69010.15231440.11862738X-RAY DIFFRACTION100
1.6901-1.72680.16581430.11862705X-RAY DIFFRACTION100
1.7268-1.7670.1661420.12042696X-RAY DIFFRACTION100
1.767-1.81120.1761430.12192719X-RAY DIFFRACTION99
1.8112-1.86020.14151420.1182698X-RAY DIFFRACTION99
1.8602-1.91490.15841420.11572701X-RAY DIFFRACTION99
1.9149-1.97670.15461410.11612685X-RAY DIFFRACTION99
1.9767-2.04740.1721420.11832689X-RAY DIFFRACTION99
2.0474-2.12930.14531420.11812693X-RAY DIFFRACTION99
2.1293-2.22620.16841430.12122726X-RAY DIFFRACTION99
2.2262-2.34360.16071420.12772700X-RAY DIFFRACTION99
2.3436-2.49040.15831410.12752666X-RAY DIFFRACTION98
2.4904-2.68270.15871420.13372700X-RAY DIFFRACTION98
2.6827-2.95260.14011390.13552639X-RAY DIFFRACTION96
2.9526-3.37970.1531410.1352685X-RAY DIFFRACTION98
3.3797-4.25750.14261420.12272696X-RAY DIFFRACTION97
4.2575-43.620.14591440.14922730X-RAY DIFFRACTION97

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