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- PDB-5uti: Crystal Structure of TGT in complex with fragment in preQ1 pocket -

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Basic information

Entry
Database: PDB / ID: 5uti
TitleCrystal Structure of TGT in complex with fragment in preQ1 pocket
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA / Guanine exchange enzyme / preq1 pocket / guanine pocket
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
L-CANAVANINE / TRIETHYLENE GLYCOL / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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: RCSB / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)42,4286
Polymers41,7631
Non-polymers6645
Water4,846269
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,85512
Polymers83,5272
Non-polymers1,32810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area6030 Å2
ΔGint9 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.158, 64.322, 70.851
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-753-

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 subsp. mobilis ZM4 = ATCC 31821 (bacteria)
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, 274 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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
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
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→44.513 Å / Num. obs: 81480 / % possible obs: 95 % / Redundancy: 2.9 % / Rsym value: 0.05 / Net I/σ(I): 11.56
Reflection shellResolution: 1.36→1.44 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.31 / % possible all: 92.5

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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: 1.36→44.513 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1582 4071 5 %
Rwork0.1345 --
obs0.1356 81466 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→44.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 40 269 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073051
X-RAY DIFFRACTIONf_angle_d0.9484119
X-RAY DIFFRACTIONf_dihedral_angle_d23.5151155
X-RAY DIFFRACTIONf_chiral_restr0.071431
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3601-1.37620.2781310.25312503X-RAY DIFFRACTION89
1.3762-1.39290.27641340.23012568X-RAY DIFFRACTION92
1.3929-1.41060.22741390.21152641X-RAY DIFFRACTION94
1.4106-1.42910.24851370.19822589X-RAY DIFFRACTION94
1.4291-1.44870.24621400.18612653X-RAY DIFFRACTION94
1.4487-1.46940.21791370.17322610X-RAY DIFFRACTION94
1.4694-1.49130.1911400.15122661X-RAY DIFFRACTION95
1.4913-1.51460.18231380.14352623X-RAY DIFFRACTION94
1.5146-1.53950.19231400.13342652X-RAY DIFFRACTION94
1.5395-1.5660.15871360.12742599X-RAY DIFFRACTION93
1.566-1.59450.15671390.12292628X-RAY DIFFRACTION95
1.5945-1.62520.14591410.12082682X-RAY DIFFRACTION95
1.6252-1.65830.16011410.11912672X-RAY DIFFRACTION95
1.6583-1.69440.13761390.11522654X-RAY DIFFRACTION95
1.6944-1.73380.15431430.11312704X-RAY DIFFRACTION96
1.7338-1.77720.13961420.11282704X-RAY DIFFRACTION96
1.7772-1.82520.13481420.11142693X-RAY DIFFRACTION96
1.8252-1.87890.1441400.11352669X-RAY DIFFRACTION96
1.8789-1.93960.15271430.11542712X-RAY DIFFRACTION96
1.9396-2.00890.14521410.11342684X-RAY DIFFRACTION96
2.0089-2.08940.14841420.11492705X-RAY DIFFRACTION96
2.0894-2.18440.14331390.11582641X-RAY DIFFRACTION94
2.1844-2.29960.11741450.11622745X-RAY DIFFRACTION97
2.2996-2.44370.14031420.11362705X-RAY DIFFRACTION97
2.4437-2.63230.14771440.12872730X-RAY DIFFRACTION97
2.6323-2.89720.14261440.13532740X-RAY DIFFRACTION97
2.8972-3.31630.18011430.14982711X-RAY DIFFRACTION96
3.3163-4.17770.1591440.13642736X-RAY DIFFRACTION95
4.1777-44.53680.16521450.15722781X-RAY DIFFRACTION96

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