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

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Basic information

Entry
Database: PDB / ID: 5jsv
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3aR,4R,6R,6aR)-6-methoxy-2,2-dimethyltetrahydrofuro[3,4-d][1,3]dioxol-4-yl)methyl)amino)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / co-crystallization / carbohydrates / 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-6MQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsEhrmann, F.R. / Nguyen, D. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Application of carbohydrates based lin-benzoguanines in a solvent-exposed subpocket of the tRNA-modifying Enzyme TGT
Authors: Ehrmann, F.R. / Schaefer, E. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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)43,7057
Polymers42,9261
Non-polymers7806
Water8,323462
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,41114
Polymers85,8512
Non-polymers1,55912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5110 Å2
ΔGint-42 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.505, 65.200, 70.598
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-923-

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 ZM4 = ATCC 31821 (bacteria)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 468 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-6MQ / methyl 5-[(6-amino-8-oxo-7,8-dihydro-3H-imidazo[4,5-g]quinazolin-2-yl)amino]-5-deoxy-2,3-O-(1-methylethylidene)-beta-D-ribofuranoside


Mass: 402.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
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: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.17→43.58 Å / Num. obs: 134123 / % possible obs: 97.4 % / Redundancy: 4 % / Rsym value: 0.037 / Net I/σ(I): 19
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.3 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1492refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.17→39.948 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.33
RfactorNum. reflection% reflectionSelection details
Rfree0.1394 6706 5 %random selected
Rwork0.1211 ---
obs0.122 134119 97.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→39.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 49 462 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053212
X-RAY DIFFRACTIONf_angle_d0.8614361
X-RAY DIFFRACTIONf_dihedral_angle_d22.9971238
X-RAY DIFFRACTIONf_chiral_restr0.074451
X-RAY DIFFRACTIONf_plane_restr0.006611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1686-1.18180.20831750.17333321X-RAY DIFFRACTION76
1.1818-1.19570.17512090.15833964X-RAY DIFFRACTION91
1.1957-1.21030.1872190.15554168X-RAY DIFFRACTION95
1.2103-1.22560.15652190.14284166X-RAY DIFFRACTION97
1.2256-1.24180.14732240.13424240X-RAY DIFFRACTION97
1.2418-1.25880.14792240.12774260X-RAY DIFFRACTION98
1.2588-1.27680.13742240.12534255X-RAY DIFFRACTION98
1.2768-1.29580.15112260.12044300X-RAY DIFFRACTION99
1.2958-1.31610.13292260.11914284X-RAY DIFFRACTION98
1.3161-1.33770.13762250.11464276X-RAY DIFFRACTION99
1.3377-1.36070.15022280.11064337X-RAY DIFFRACTION99
1.3607-1.38550.12172240.10674265X-RAY DIFFRACTION99
1.3855-1.41210.12832250.10564267X-RAY DIFFRACTION99
1.4121-1.44090.13492250.10614280X-RAY DIFFRACTION98
1.4409-1.47230.13722260.10074285X-RAY DIFFRACTION98
1.4723-1.50650.11692250.09394288X-RAY DIFFRACTION98
1.5065-1.54420.10962260.09084282X-RAY DIFFRACTION99
1.5442-1.58590.11632260.09414290X-RAY DIFFRACTION98
1.5859-1.63260.12222280.09584330X-RAY DIFFRACTION99
1.6326-1.68530.11962260.10324300X-RAY DIFFRACTION99
1.6853-1.74560.13422260.10944295X-RAY DIFFRACTION99
1.7456-1.81540.12212260.11114305X-RAY DIFFRACTION99
1.8154-1.89810.13832260.11244292X-RAY DIFFRACTION99
1.8981-1.99810.12842310.11774375X-RAY DIFFRACTION99
1.9981-2.12330.14292250.12094287X-RAY DIFFRACTION99
2.1233-2.28720.13032280.1244322X-RAY DIFFRACTION98
2.2872-2.51740.14072270.12654310X-RAY DIFFRACTION98
2.5174-2.88160.14612270.13314313X-RAY DIFFRACTION99
2.8816-3.63010.14262290.12574369X-RAY DIFFRACTION99
3.6301-39.97130.15442310.13424387X-RAY DIFFRACTION98

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