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- PDB-6h42: crystal structure of the human TGT catalytic subunit QTRT1 -

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Basic information

Entry
Database: PDB / ID: 6h42
Titlecrystal structure of the human TGT catalytic subunit QTRT1
ComponentsQueuine tRNA-ribosyltransferase catalytic subunit 1
KeywordsTRANSFERASE / transglycosylase / queuine / tRNA
Function / homology
Function and homology information


tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / protein-containing complex ...tRNA-guanosine34 queuine transglycosylase / transferase complex / tRNA modification in the nucleus and cytosol / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / tRNA modification / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / metal ion binding / nucleus
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
BROMIDE ION / GLUTAMIC ACID / : / Queuine tRNA-ribosyltransferase catalytic subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsJohannsson, S. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP 1784 Germany
CitationJournal: Biomolecules / Year: 2018
Title: Crystal Structure of the Human tRNA Guanine Transglycosylase Catalytic Subunit QTRT1.
Authors: Johannsson, S. / Neumann, P. / Ficner, R.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_special_symmetry.auth_comp_id / _pdbx_struct_special_symmetry.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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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)87,26219
Polymers86,3912
Non-polymers87017
Water1,78399
1
A: Queuine tRNA-ribosyltransferase catalytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5579
Polymers43,1961
Non-polymers3628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Queuine tRNA-ribosyltransferase catalytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70410
Polymers43,1961
Non-polymers5099
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.700, 157.820, 47.770
Angle α, β, γ (deg.)90.000, 108.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-506-

CL

21B-507-

CL

31B-508-

BR

41B-509-

GLU

51B-601-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 43195.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QTRT1, TGT, TGUT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BXR0, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 116 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 7.8 200 mM KBr 200 mM KSCN 3 % (w/v) PGA-LM 5 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.45→48.253 Å / Num. obs: 64817 / % possible obs: 99.4 % / Redundancy: 4.491 % / Biso Wilson estimate: 52.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.106 / Χ2: 0.978 / Net I/σ(I): 10.29 / Num. measured all: 291113 / Scaling rejects: 671
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.554.5210.9821.6833232738773510.5991.11299.5
2.55-2.654.4950.7262.2428314632762990.7490.82399.6
2.65-2.854.5010.4943.18449511003199870.8660.55999.6
2.85-84.4840.07614.317637039606393340.9970.08799.3
8-144.5130.05925.246756150414970.9960.06699.5
14-174.5340.06125.417301671610.990.0796.4
17-504.0430.08323.327601911880.9830.09798.4
48.253-505

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.253 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1644 5 %
Rwork0.2024 31206 -
obs0.2038 32850 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.92 Å2 / Biso mean: 67.1975 Å2 / Biso min: 34.38 Å2
Refinement stepCycle: final / Resolution: 2.45→48.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6025 0 26 99 6150
Biso mean--76.17 57.17 -
Num. residues----784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.52210.32961380.308626032741100
2.5221-2.60350.35181360.282425822718100
2.6035-2.69650.27071360.26725832719100
2.6965-2.80450.31821380.259626182756100
2.8045-2.93210.3071360.25525782714100
2.9321-3.08670.27841360.251325842720100
3.0867-3.280.27231370.23626022739100
3.28-3.53320.26181370.215225982735100
3.5332-3.88860.25551370.200726102747100
3.8886-4.4510.17561370.164226102747100
4.451-5.60640.18691370.162225942731100
5.6064-48.2620.18941390.1752644278399
Refinement TLS params.Method: refined / Origin x: 11.6145 Å / Origin y: -22.8634 Å / Origin z: 66.8316 Å
111213212223313233
T0.3759 Å20.0222 Å20.0065 Å2-0.517 Å2-0.0191 Å2--0.3903 Å2
L0.0394 °20.1285 °2-0.1006 °2-1.7219 °2-0.2362 °2--0.4629 °2
S0.0167 Å °-0.0676 Å °-0.0479 Å °0.0004 Å °-0.0206 Å °-0.0131 Å °0.0282 Å °0.3067 Å °0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 403
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB13 - 403
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allC2 - 3
6X-RAY DIFFRACTION1allE3 - 12
7X-RAY DIFFRACTION1allE13 - 16
8X-RAY DIFFRACTION1allS2 - 155
9X-RAY DIFFRACTION1allS156 - 160
10X-RAY DIFFRACTION1allF6
11X-RAY DIFFRACTION1allF7
12X-RAY DIFFRACTION1allH1

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