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- PDB-5n6f: Crystal structure of TGT in complex with guanine fragment -

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Basic information

Entry
Database: PDB / ID: 5n6f
TitleCrystal structure of TGT in complex with guanine fragment
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA / GUANINE EXCHANGE ENZYME / TRANSGLYCOSYLASE
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine 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
GUANINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11909520042 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: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 2.0Dec 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / cell / computing / diffrn / diffrn_radiation_wavelength / entity / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conn / struct_mon_prot_cis / struct_site_gen / symmetry
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta ..._atom_sites.fract_transf_matrix[1][3] / _cell.angle_beta / _cell.volume / _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_low / _reflns_shell.number_unique_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site_gen.auth_seq_id / _symmetry.space_group_name_Hall
Description: Model completeness
Details: addition of residue 158 and review of problematic water molecules.
Provider: author / Type: Coordinate replacement
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 / 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)42,3146
Polymers41,7631
Non-polymers5515
Water5,026279
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,62912
Polymers83,5272
Non-polymers1,10210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5120 Å2
ΔGint6 kcal/mol
Surface area26140 Å2
Unit cell
Length a, b, c (Å)88.711, 64.851, 70.655
Angle α, β, γ (deg.)90.000, 93.357, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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 , 6 types, 284 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 13% PEG8000, 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: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.119→44.28 Å / Num. obs: 149008 / % possible obs: 97.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.8545945983 Å2 / Rsym value: 0.061 / Net I/σ(I): 10.3
Reflection shellResolution: 1.119→1.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 149008 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LBU

4lbu


Resolution: 1.11909520042→44.2793884339 Å / SU ML: 0.0973131262279 / Cross valid method: FREE R-VALUE / σ(F): 1.3545538695 / Phase error: 13.5056770047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.153498297959 7451 5.00077182762 %
Rwork0.135902777855 141546 -
obs0.136782737006 148997 97.0506432177 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8179302453 Å2
Refinement stepCycle: LAST / Resolution: 1.11909520042→44.2793884339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 33 279 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006525221040142986
X-RAY DIFFRACTIONf_angle_d0.9621725675894034
X-RAY DIFFRACTIONf_chiral_restr0.0742712069091425
X-RAY DIFFRACTIONf_plane_restr0.00657054679121549
X-RAY DIFFRACTIONf_dihedral_angle_d22.76424058681119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1191-1.13180.3279959932461710.3140100523883248X-RAY DIFFRACTION68.053343949
1.1318-1.14510.3007693138331970.2666546280453749X-RAY DIFFRACTION76.890101325
1.1451-1.15910.256653054952150.2345948334069X-RAY DIFFRACTION83.671875
1.1591-1.17380.2051481906092290.2160320130184360X-RAY DIFFRACTION90.5664101046
1.1738-1.18920.2256111258542530.1923958852344796X-RAY DIFFRACTION99.2920353982
1.1892-1.20550.1883973656022520.1727977557914807X-RAY DIFFRACTION99.8027224305
1.2055-1.22270.1922917516942590.1674663398514905X-RAY DIFFRACTION99.8839458414
1.2227-1.2410.1791303664582530.1587324792944821X-RAY DIFFRACTION99.8818897638
1.241-1.26040.1634121239742540.1503516108984825X-RAY DIFFRACTION99.8820058997
1.2604-1.2810.1546145344942570.1428437892424866X-RAY DIFFRACTION99.8051821547
1.281-1.30310.1712021969972530.1414543328114820X-RAY DIFFRACTION99.7640117994
1.3031-1.32680.1668157052362550.134406099894832X-RAY DIFFRACTION99.7646597372
1.3268-1.35240.1551618498972550.1283609664984843X-RAY DIFFRACTION99.9411880024
1.3524-1.380.1637322259882550.1322554371444851X-RAY DIFFRACTION99.8435666797
1.38-1.410.1419927802112580.1189375567224901X-RAY DIFFRACTION99.9225256634
1.41-1.44280.1395499455022530.1173742903394810X-RAY DIFFRACTION99.9210578251
1.4428-1.47880.1382571995652560.1093737140524858X-RAY DIFFRACTION99.7853658537
1.4788-1.51880.1178696813512520.1061198583734797X-RAY DIFFRACTION99.7037914692
1.5188-1.56350.1212376017782550.1056464949714846X-RAY DIFFRACTION99.7457958545
1.5635-1.6140.1238988524352570.1042175439844883X-RAY DIFFRACTION99.8639984457
1.614-1.67170.1269058746672550.1064440202434842X-RAY DIFFRACTION99.7455968689
1.6717-1.73860.1345712402012540.1096143398234829X-RAY DIFFRACTION99.7253286247
1.7386-1.81770.1181415678172560.1132658019524863X-RAY DIFFRACTION99.688412853
1.8177-1.91360.1401070900792560.1157792852064857X-RAY DIFFRACTION99.5909622127
1.9136-2.03350.1248678198342570.1160108140314876X-RAY DIFFRACTION99.5539177657
2.0335-2.19050.1334377601732540.1167927917444836X-RAY DIFFRACTION99.5696400626
2.1905-2.41090.1506749553752560.1210245924884861X-RAY DIFFRACTION99.5719011481
2.4109-2.75970.1349296013232560.1271247268564875X-RAY DIFFRACTION99.3417231365
2.7597-3.47670.1596239549422560.1469239133474863X-RAY DIFFRACTION99.4366744367
3.4767-44.270.1807162909222620.1639226508064957X-RAY DIFFRACTION98.9383886256

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