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- PDB-5utj: Crystal Structure of TGT in complex with 2,6-dioxy-8-azapurine, 2... -

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Basic information

Entry
Database: PDB / ID: 5utj
TitleCrystal Structure of TGT in complex with 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine, 2,6-dioxy-8-azapurine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / tRNA / guanine exchange enzyme / transglycosylase / fragments
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
8-AZAXANTHINE / DI(HYDROXYETHYL)ETHER / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2020
Title: Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies.
Authors: Hassaan, E. / Eriksson, P.O. / Geschwindner, S. / Heine, A. / Klebe, G.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 26, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_detector / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _diffrn_detector.detector / _diffrn_detector.type
Revision 2.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)42,2726
Polymers41,7631
Non-polymers5095
Water3,243180
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,54512
Polymers83,5272
Non-polymers1,01810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4370 Å2
ΔGint-8 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.142, 64.759, 70.451
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

PEG

21A-549-

HOH

31A-673-

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: 41763.484 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 / Plasmid: PPR-IBA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-AZA / 8-AZAXANTHINE


Mass: 153.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3N5O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting 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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.549→44.503 Å / Num. obs: 58080 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rsym value: 0.052 / Net I/σ(I): 15.35
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LBU

4lbu


Resolution: 1.549→44.503 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 2904 5 %
Rwork0.1473 --
obs0.1488 58069 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.549→44.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 30 180 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082964
X-RAY DIFFRACTIONf_angle_d0.9494002
X-RAY DIFFRACTIONf_dihedral_angle_d17.8821806
X-RAY DIFFRACTIONf_chiral_restr0.053419
X-RAY DIFFRACTIONf_plane_restr0.006548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.549-1.57440.32311370.26932603X-RAY DIFFRACTION98
1.5744-1.60150.28921370.21722604X-RAY DIFFRACTION100
1.6015-1.63060.29841360.20862594X-RAY DIFFRACTION100
1.6306-1.6620.2051390.18552634X-RAY DIFFRACTION100
1.662-1.69590.21541370.17052594X-RAY DIFFRACTION100
1.6959-1.73280.22521380.16852633X-RAY DIFFRACTION100
1.7328-1.77310.21941390.14972642X-RAY DIFFRACTION100
1.7731-1.81750.17491360.1432584X-RAY DIFFRACTION100
1.8175-1.86660.2081390.14442633X-RAY DIFFRACTION100
1.8666-1.92150.19731360.14232599X-RAY DIFFRACTION100
1.9215-1.98360.16231400.12692653X-RAY DIFFRACTION100
1.9836-2.05440.15291380.12242614X-RAY DIFFRACTION100
2.0544-2.13670.1461390.11342638X-RAY DIFFRACTION100
2.1367-2.23390.14131380.11322637X-RAY DIFFRACTION100
2.2339-2.35170.15031380.11332613X-RAY DIFFRACTION100
2.3517-2.4990.16831400.12382654X-RAY DIFFRACTION100
2.499-2.6920.15941370.13282618X-RAY DIFFRACTION100
2.692-2.96280.16511390.14122633X-RAY DIFFRACTION100
2.9628-3.39140.18591390.15922646X-RAY DIFFRACTION100
3.3914-4.27230.15621400.14952658X-RAY DIFFRACTION99
4.2723-44.52180.18331420.16962681X-RAY DIFFRACTION99

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