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- PDB-6h62: QTRT1, the catalytic subunit of murine tRNA-Guanine Transglycosylase -

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Basic information

Entry
Database: PDB / ID: 6h62
TitleQTRT1, the catalytic subunit of murine tRNA-Guanine Transglycosylase
ComponentsQueuine tRNA-ribosyltransferase catalytic subunit 1
KeywordsTRANSFERASE / Transglycosylase / TIM Barrel
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / metal ion binding / nucleus / cytoplasm
Similarity search - Function
tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase catalytic subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.684 Å
AuthorsBehrens, C. / Heine, A. / Reuter, K.
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase.
Authors: Sebastiani, M. / Behrens, C. / Dorr, S. / Gerber, H.D. / Benazza, R. / Hernandez-Alba, O. / Cianferani, S. / Klebe, G. / Heine, A. / Reuter, K.
History
DepositionJul 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _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 catalytic subunit 1
B: Queuine tRNA-ribosyltransferase catalytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6076
Polymers88,2922
Non-polymers3154
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, 20% Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-14 kcal/mol
Surface area29740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.704, 93.767, 117.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Queuine tRNA-ribosyltransferase catalytic subunit 1 / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 44145.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qtrt1, Tgt, Tgut / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JMA2, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100mM CAPS pH 10.5, 200 mM Sodium chloride, 20% PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.111.282814
SYNCHROTRONBESSY 14.121.283345
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 7, 2018
DECTRIS PILATUS 6M2PIXELApr 7, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.2828141
21.2833451
Reflection

Entry-ID: 6H62

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rsym valueDiffraction-IDNet I/σ(I)
2.68-504960899.76.980.121113.95
3.42-502401599.17.10.194211.81
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRsym valueDiffraction-ID
2.68-2.856.98379180.6631
3.42-3.636.93.737190.7241

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
XDSdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.684→47.985 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 2054 4.14 %
Rwork0.1868 --
obs0.1886 49585 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.684→47.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5394 0 14 84 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025517
X-RAY DIFFRACTIONf_angle_d0.457503
X-RAY DIFFRACTIONf_dihedral_angle_d13.2413291
X-RAY DIFFRACTIONf_chiral_restr0.038881
X-RAY DIFFRACTIONf_plane_restr0.005964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6841-2.74650.2781280.24683046X-RAY DIFFRACTION97
2.7465-2.81520.30241350.2313189X-RAY DIFFRACTION100
2.8152-2.89130.31091370.22553185X-RAY DIFFRACTION100
2.8913-2.97640.26671340.22263159X-RAY DIFFRACTION100
2.9764-3.07240.24381430.21923197X-RAY DIFFRACTION100
3.0724-3.18220.24411410.21133159X-RAY DIFFRACTION100
3.1822-3.30960.2481380.2063195X-RAY DIFFRACTION100
3.3096-3.46020.23211350.19393170X-RAY DIFFRACTION100
3.4602-3.64260.23541390.18633195X-RAY DIFFRACTION100
3.6426-3.87070.2131400.1733149X-RAY DIFFRACTION100
3.8707-4.16940.2021380.15393214X-RAY DIFFRACTION100
4.1694-4.58870.18161330.14763157X-RAY DIFFRACTION100
4.5887-5.25190.21331370.15273184X-RAY DIFFRACTION99
5.2519-6.61410.22571360.20633181X-RAY DIFFRACTION100
6.6141-47.99260.22151400.19483151X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2621-0.3912-0.43641.7156-0.361.8370.08670.0775-0.4739-0.1117-0.0726-0.07710.02830.00260.00540.2773-0.01730.00150.28240.03310.30257.958250.857141.3336
20.8512-0.01480.04182.602-0.78130.86950.063-0.2747-0.49390.3071-0.1716-0.29830.12810.08810.10730.323-0.0557-0.07060.38380.14880.511161.511839.577154.2235
32.98420.16130.39231.77910.28362.02130.0432-0.33320.06050.1303-0.19720.3271-0.2955-0.3160.14840.36830.0034-0.01190.3913-0.04570.320944.699261.451150.5776
41.97910.06460.68771.34820.00312.0953-0.12790.05710.1591-0.2413-0.03890.0443-0.28660.11730.16150.33720.0099-0.03780.26510.00620.249922.10136.399323.155
51.3786-1.449-0.50931.82080.97990.4717-0.2275-0.2880.6565-0.09310.3054-0.1751-0.42830.1659-0.05290.5820.0903-0.10210.47960.0350.553621.469353.561328.1204
60.9819-0.21350.18672.9016-0.69871.5629-0.05380.09640.2689-0.0688-0.05460.4207-0.3116-0.08880.09340.32220.0595-0.0840.2739-0.00690.3479.115448.11927.3639
72.19551.17210.41730.9578-0.22811.8990.1785-0.1902-0.18230.0676-0.2904-0.1430.04580.14070.08370.2937-0.0133-0.06360.26740.04620.272122.774927.02239.1292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 273 )
3X-RAY DIFFRACTION3chain 'A' and (resid 274 through 402 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 91 )
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 128 through 273 )
7X-RAY DIFFRACTION7chain 'B' and (resid 274 through 403 )

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