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- PDB-6rkt: Crystal Structure of TGT in complex with N2-methyl-1H,7H,8H-imida... -

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Basic information

Entry
Database: PDB / ID: 6rkt
TitleCrystal Structure of TGT in complex with N2-methyl-1H,7H,8H-imidazo[4,5-g]quinazoline-2,6-diamine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA / GUANINE EXCHANGE ENZYME / PROTEIN INTERFACE / transglycosylase
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
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Chem-K7H / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.746 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT.
Authors: Hassaan, E. / Hohn, C. / Ehrmann, F.R. / Goetzke, F.W. / Movsisyan, L. / Hufner-Wulsdorf, T. / Sebastiani, M. / Hartsch, A. / Reuter, K. / Diederich, F. / Klebe, G.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)42,2155
Polymers41,7631
Non-polymers4524
Water3,459192
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,43110
Polymers83,5272
Non-polymers9048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3910 Å2
ΔGint-15 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.629, 64.588, 71.176
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-683-

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 (bacteria) / Gene: tgt, ZMO0363 / Variant: ATCC 31821 / ZM4 / CP4 / 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, 196 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K7H / ~{N}2-methyl-7,8-dihydro-3~{H}-imidazo[4,5-g]quinazoline-2,6-diamine


Mass: 216.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 49.76 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.746→44.738 Å / Num. obs: 40353 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rsym value: 0.035 / Net I/σ(I): 17.56
Reflection shellResolution: 1.746→1.754 Å / Num. unique obs: 6118 / % possible all: 97.7

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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: 1.746→38.895 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 2014 5 %
Rwork0.1695 --
obs0.1712 40307 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.746→38.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 27 192 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092895
X-RAY DIFFRACTIONf_angle_d0.9973904
X-RAY DIFFRACTIONf_dihedral_angle_d14.5261744
X-RAY DIFFRACTIONf_chiral_restr0.054412
X-RAY DIFFRACTIONf_plane_restr0.007532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7456-1.78930.33061230.31622339X-RAY DIFFRACTION84
1.7893-1.83770.32611450.27092741X-RAY DIFFRACTION98
1.8377-1.89180.28021450.24582780X-RAY DIFFRACTION100
1.8918-1.95280.27391460.23012773X-RAY DIFFRACTION100
1.9528-2.02260.26141450.20342750X-RAY DIFFRACTION100
2.0226-2.10360.23651470.18632794X-RAY DIFFRACTION100
2.1036-2.19930.22221460.18122786X-RAY DIFFRACTION99
2.1993-2.31520.24091450.17612766X-RAY DIFFRACTION99
2.3152-2.46030.2161450.16562754X-RAY DIFFRACTION99
2.4603-2.65020.18671450.17882753X-RAY DIFFRACTION98
2.6502-2.91680.20691450.16682756X-RAY DIFFRACTION98
2.9168-3.33870.19491410.16852664X-RAY DIFFRACTION95
3.3387-4.20560.1641480.14622814X-RAY DIFFRACTION99
4.2056-38.90510.19511480.15212823X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2184-0.3997-0.27070.0281-0.00731.2946-0.041-0.0176-0.00450.08350.0459-0.0082-0.0557-0.0162-00.33880.01770.00380.2296-0.00780.30494.62370.324889.4741
20.0420.0057-0.02460.0147-0.00770.0322-0.2264-0.33960.2240.0161-0.1184-0.21870.0895-0.3579-0.00060.80210.0692-0.14320.4345-0.14570.592.74522.833699.7773
30.11770.05150.18350.00620.04360.2059-0.0437-0.34250.1690.13820.063-0.0273-0.2992-0.065400.42070.0234-0.00320.3539-0.0570.30542.20789.2242100.7827
40.5611-0.4839-0.11840.4170.25770.5666-0.0255-0.52960.13640.16280.0881-0.1122-0.18490.24350.01810.3855-0.0412-0.02610.4173-0.09080.324414.91789.6959103.8439
50.69090.0415-0.51710.73750.50260.6560.0402-0.16510.2279-0.05030.1105-0.1582-0.15880.1520.00020.3196-0.0344-0.00030.3541-0.0350.375721.53016.62389.3346
60.472-0.5090.9201-0.0788-0.47850.98950.01360.1965-0.0296-0.0395-0.0237-0.00340.01550.209200.34310.00610.01950.32780.0080.308613.53693.149268.7075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 284 )
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 383 )

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