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- PDB-6ygm: TGT W95F mutant labelled mit 5F-Trp crystallised at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6ygm
TitleTGT W95F 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-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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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)43,1502
Polymers43,0851
Non-polymers651
Water6,017334
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3004
Polymers86,1702
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2060 Å2
ΔGint-16 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.536, 64.970, 71.251
Angle α, β, γ (deg.)90.000, 93.996, 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

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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)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
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: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.23→42.17 Å / Num. obs: 107425 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.31 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.11
Reflection shellResolution: 1.23→1.31 Å / Num. unique obs: 16748 / CC1/2: 0.842

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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: 1.23→42.17 Å / SU ML: 0.1062 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.8193
RfactorNum. reflection% reflection
Rfree0.1598 5371 5 %
Rwork0.1357 --
obs0.137 107396 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.31 Å2
Refinement stepCycle: LAST / Resolution: 1.23→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 1 334 3028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692856
X-RAY DIFFRACTIONf_angle_d0.93233877
X-RAY DIFFRACTIONf_chiral_restr0.0675411
X-RAY DIFFRACTIONf_plane_restr0.0065523
X-RAY DIFFRACTIONf_dihedral_angle_d21.53231037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.250.26091610.2293064X-RAY DIFFRACTION89.01
1.25-1.260.23711760.22093344X-RAY DIFFRACTION96.52
1.26-1.280.2861760.22013339X-RAY DIFFRACTION96.33
1.28-1.290.21731770.19393356X-RAY DIFFRACTION96.06
1.29-1.310.21581730.18843286X-RAY DIFFRACTION95.11
1.31-1.330.19761780.18083390X-RAY DIFFRACTION96.8
1.33-1.350.21541760.17053339X-RAY DIFFRACTION97.29
1.35-1.370.21191810.16463436X-RAY DIFFRACTION97.76
1.37-1.390.17071760.15573350X-RAY DIFFRACTION97.59
1.39-1.410.18091790.15053405X-RAY DIFFRACTION97.36
1.41-1.440.18991810.14453439X-RAY DIFFRACTION97.81
1.44-1.460.16881790.1353387X-RAY DIFFRACTION97.99
1.46-1.490.17981790.12863397X-RAY DIFFRACTION97.81
1.49-1.520.16091790.12423409X-RAY DIFFRACTION96.79
1.52-1.560.16831750.11343319X-RAY DIFFRACTION96.49
1.56-1.590.13911780.11243380X-RAY DIFFRACTION98.1
1.59-1.630.1361820.10663470X-RAY DIFFRACTION98.3
1.63-1.680.13691780.11113382X-RAY DIFFRACTION98.37
1.68-1.720.15741840.11213484X-RAY DIFFRACTION98.6
1.72-1.780.14341820.11643458X-RAY DIFFRACTION98.97
1.78-1.840.15251810.11823444X-RAY DIFFRACTION98.83
1.84-1.920.15921770.11853370X-RAY DIFFRACTION97.02
1.92-2.010.14121810.11613425X-RAY DIFFRACTION98.31
2.01-2.110.1431830.11973473X-RAY DIFFRACTION99.21
2.11-2.240.13021830.12193490X-RAY DIFFRACTION99.46
2.24-2.420.15011840.12023488X-RAY DIFFRACTION99.27
2.42-2.660.13171820.12873467X-RAY DIFFRACTION99.08
2.66-3.040.16021790.13513403X-RAY DIFFRACTION97.31
3.04-3.840.16751860.13223521X-RAY DIFFRACTION99.28
3.84-42.170.1681850.16473510X-RAY DIFFRACTION97.88

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