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- PDB-6ygo: TGT W95F mutant labelled mit 5F-Trp crystallised at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 6ygo
TitleTGT W95F mutant labelled mit 5F-Trp crystallised at pH 8.5
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / HOMODIMER / 19F-NMR / 5F-TRP
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
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
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Mutation study on tRNA-guanine transglycosylase within 19F NMR experiments for conformational change analysis
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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)43,5196
Polymers43,0851
Non-polymers4345
Water6,377354
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,03712
Polymers86,1702
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)90.839, 64.927, 70.749
Angle α, β, γ (deg.)90.000, 96.031, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-828-

HOH

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Components

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


Mass: 43084.766 Da / Num. of mol.: 1 / Mutation: T312K
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 / Production host: Escherichia coli (E. coli) / Strain (production host): 62077
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM TRIS pH 8.5, 1 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.26→43.49 Å / Num. obs: 109120 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.13 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.22
Reflection shellResolution: 1.26→1.34 Å / Num. unique obs: 17332 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.26→43.49 Å / SU ML: 0.1019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.1414
RfactorNum. reflection% reflection
Rfree0.1451 5455 5 %
Rwork0.1224 --
obs0.1235 109106 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.16 Å2
Refinement stepCycle: LAST / Resolution: 1.26→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 25 354 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693059
X-RAY DIFFRACTIONf_angle_d0.96984142
X-RAY DIFFRACTIONf_chiral_restr0.0712434
X-RAY DIFFRACTIONf_plane_restr0.0064558
X-RAY DIFFRACTIONf_dihedral_angle_d22.91671136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.270.24541740.22353311X-RAY DIFFRACTION94.24
1.27-1.290.21161780.19993400X-RAY DIFFRACTION98.51
1.29-1.30.22221800.19983416X-RAY DIFFRACTION97.32
1.3-1.320.18761760.18923337X-RAY DIFFRACTION96.78
1.32-1.340.21731830.17453484X-RAY DIFFRACTION99.46
1.34-1.360.19451840.17393486X-RAY DIFFRACTION99.54
1.36-1.380.1891810.16473445X-RAY DIFFRACTION99.18
1.38-1.40.19971830.15983481X-RAY DIFFRACTION99.13
1.4-1.420.16741810.14653436X-RAY DIFFRACTION99.37
1.42-1.440.18191840.1343488X-RAY DIFFRACTION99.27
1.44-1.470.16541800.12723424X-RAY DIFFRACTION98.96
1.47-1.490.14291810.11363447X-RAY DIFFRACTION98.72
1.49-1.520.15471790.11183391X-RAY DIFFRACTION97.92
1.52-1.550.1441800.10723433X-RAY DIFFRACTION97.57
1.55-1.590.12411820.10213452X-RAY DIFFRACTION99.7
1.59-1.620.13591840.09713499X-RAY DIFFRACTION99.84
1.62-1.660.12351830.10033469X-RAY DIFFRACTION99.78
1.66-1.710.14351840.10293495X-RAY DIFFRACTION99.54
1.71-1.760.12631820.09933467X-RAY DIFFRACTION99.35
1.76-1.820.13411830.10033467X-RAY DIFFRACTION98.89
1.82-1.880.11531810.10463442X-RAY DIFFRACTION98.26
1.88-1.960.13951790.10023400X-RAY DIFFRACTION97.39
1.96-2.040.11581830.10313475X-RAY DIFFRACTION99.73
2.04-2.150.11121840.10293501X-RAY DIFFRACTION99.46
2.15-2.290.1321830.10693484X-RAY DIFFRACTION99.43
2.29-2.460.12541850.10593504X-RAY DIFFRACTION99.41
2.46-2.710.13251810.11963442X-RAY DIFFRACTION98.59
2.71-3.10.12461850.1243510X-RAY DIFFRACTION99.19
3.1-3.910.16291840.123504X-RAY DIFFRACTION99.03
3.91-43.490.16721880.15273561X-RAY DIFFRACTION98.81

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