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- PDB-6ygp: TGT WT labelled mit 5F-Trp crystallised at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6ygp
TitleTGT WT 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-guanine transglycosylation / queuosine 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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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
Polymers43,1421
Non-polymers3775
Water6,792377
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,03812
Polymers86,2842
Non-polymers75410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)90.822, 65.164, 70.547
Angle α, β, γ (deg.)90.000, 96.091, 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-819-

HOH

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Components

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


Mass: 43141.789 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / 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-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 377 / 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: 48.87 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES pH 5.5, 0.5 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: Sep 5, 2017
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: 1.33→45.15 Å / Num. obs: 90420 / % possible obs: 96.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 1.33→1.41 Å / Num. unique obs: 13633 / CC1/2: 0.835

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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: 1.33→45.15 Å / SU ML: 0.1252 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.9593
RfactorNum. reflection% reflection
Rfree0.1479 4520 5 %
Rwork0.1213 --
obs0.1226 90417 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.33→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 20 377 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072996
X-RAY DIFFRACTIONf_angle_d0.96994061
X-RAY DIFFRACTIONf_chiral_restr0.0725429
X-RAY DIFFRACTIONf_plane_restr0.0064545
X-RAY DIFFRACTIONf_dihedral_angle_d23.9041110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.340.26721160.27132212X-RAY DIFFRACTION75.93
1.34-1.360.27351390.24182646X-RAY DIFFRACTION87.85
1.36-1.380.19481460.19132760X-RAY DIFFRACTION94.66
1.38-1.390.20721520.17152891X-RAY DIFFRACTION96.88
1.39-1.410.20841520.1582897X-RAY DIFFRACTION97.16
1.41-1.430.1651510.13992860X-RAY DIFFRACTION96.85
1.43-1.450.17441500.13112861X-RAY DIFFRACTION97.16
1.45-1.470.14031540.12252914X-RAY DIFFRACTION96.97
1.47-1.50.15061490.1112839X-RAY DIFFRACTION97.01
1.5-1.520.12941510.11292869X-RAY DIFFRACTION97.07
1.52-1.550.13031500.10982856X-RAY DIFFRACTION95.61
1.55-1.580.141510.10632864X-RAY DIFFRACTION97.01
1.58-1.610.14241540.10692918X-RAY DIFFRACTION97.87
1.61-1.640.1221520.10382896X-RAY DIFFRACTION97.75
1.64-1.670.11941530.10222907X-RAY DIFFRACTION97.83
1.67-1.710.12521530.10482913X-RAY DIFFRACTION97.92
1.71-1.760.13491540.10222923X-RAY DIFFRACTION98.12
1.76-1.80.14871540.10012924X-RAY DIFFRACTION97.9
1.8-1.860.13321490.1022835X-RAY DIFFRACTION95.24
1.86-1.920.12671530.10132908X-RAY DIFFRACTION98.01
1.92-1.990.11941520.1072888X-RAY DIFFRACTION97.75
1.99-2.060.13941540.10872920X-RAY DIFFRACTION97.74
2.06-2.160.13591540.10252933X-RAY DIFFRACTION98.31
2.16-2.270.11531520.10692888X-RAY DIFFRACTION97.5
2.27-2.410.13931520.10712879X-RAY DIFFRACTION95.92
2.41-2.60.13531560.11262960X-RAY DIFFRACTION98.86
2.6-2.860.14231540.11982939X-RAY DIFFRACTION98.79
2.86-3.280.15691560.12512958X-RAY DIFFRACTION97.99
3.28-4.130.14631530.1222902X-RAY DIFFRACTION96.65
4.13-45.150.1841540.15412937X-RAY DIFFRACTION95.34

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