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- PDB-6ygw: TGT W178F mutant labelled mit 5F-Trp crystallised at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6ygw
TitleTGT W178F mutant labelled mit 5F-Trp crystallised at pH 5.5
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 wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
Similarity search - Function
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5246
Polymers43,0851
Non-polymers4395
Water7,458414
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,04812
Polymers86,1702
Non-polymers87910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)90.305, 65.345, 70.134
Angle α, β, γ (deg.)90.000, 95.993, 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-861-

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: 43084.766 Da / Num. of mol.: 1 / Mutation: T312K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli) / Variant (production host): 62077
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
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: Jun 1, 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: 1.16→44.91 Å / Num. obs: 130261 / % possible obs: 92.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 11.57 Å2 / CC1/2: 0.999 / Net I/σ(I): 21.18
Reflection shellResolution: 1.16→1.23 Å / Num. unique obs: 19851 / CC1/2: 0.975

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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: 1.16→44.91 Å / SU ML: 0.0662 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.6018
RfactorNum. reflection% reflection
Rfree0.1321 6512 5 %
Rwork0.1136 --
obs0.1145 130252 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.61 Å2
Refinement stepCycle: LAST / Resolution: 1.16→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 18 414 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673106
X-RAY DIFFRACTIONf_angle_d0.97734216
X-RAY DIFFRACTIONf_chiral_restr0.071444
X-RAY DIFFRACTIONf_plane_restr0.0065573
X-RAY DIFFRACTIONf_dihedral_angle_d24.06791162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.170.14671680.1333229X-RAY DIFFRACTION73.5
1.17-1.190.13622110.11494008X-RAY DIFFRACTION89.92
1.19-1.20.10792100.10653989X-RAY DIFFRACTION91.86
1.2-1.220.11722170.10924111X-RAY DIFFRACTION92.5
1.22-1.230.13512160.10524115X-RAY DIFFRACTION92.46
1.23-1.250.12312140.10164049X-RAY DIFFRACTION92.49
1.25-1.270.13072170.10674132X-RAY DIFFRACTION92.45
1.27-1.290.12272120.10524031X-RAY DIFFRACTION92
1.29-1.310.11882100.10743979X-RAY DIFFRACTION89.85
1.31-1.330.11642140.10324072X-RAY DIFFRACTION90.71
1.33-1.350.11982160.09744106X-RAY DIFFRACTION93.51
1.35-1.370.12662180.09854134X-RAY DIFFRACTION93.79
1.37-1.40.12552180.1014145X-RAY DIFFRACTION93.99
1.4-1.430.12712210.09744203X-RAY DIFFRACTION94.07
1.43-1.460.12372180.0954143X-RAY DIFFRACTION94.05
1.46-1.490.11552180.09174146X-RAY DIFFRACTION93.61
1.49-1.530.1232110.09213991X-RAY DIFFRACTION89.79
1.53-1.570.11242180.0924142X-RAY DIFFRACTION93.84
1.57-1.620.11252230.09194241X-RAY DIFFRACTION95.38
1.62-1.670.11752210.09494213X-RAY DIFFRACTION95.27
1.67-1.730.12282240.10034242X-RAY DIFFRACTION95.47
1.73-1.80.11542240.10174260X-RAY DIFFRACTION95.36
1.8-1.880.10582190.10194156X-RAY DIFFRACTION94.07
1.88-1.980.11382150.10794083X-RAY DIFFRACTION91.78
1.98-2.110.11782260.10894294X-RAY DIFFRACTION96.79
2.11-2.270.12412270.10924324X-RAY DIFFRACTION96.95
2.27-2.50.11672260.1114285X-RAY DIFFRACTION96.08
2.5-2.860.13892180.12284158X-RAY DIFFRACTION93.05
2.86-3.60.15962330.12714408X-RAY DIFFRACTION97.93
3.6-44.910.16322290.13994351X-RAY DIFFRACTION95.38

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