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- PDB-6z0d: tRNA-Guanine Transglycosylase (TGT) H333F mutant crystallised at ... -

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Basic information

Entry
Database: PDB / ID: 6z0d
TitletRNA-Guanine Transglycosylase (TGT) H333F mutant crystallised at pH 5.5
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Mutation study on tRNA-guanine transglycosylase for catalysis testing
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionMay 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,2363
Polymers43,0791
Non-polymers1582
Water6,846380
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4736
Polymers86,1582
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3340 Å2
ΔGint-21 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.791, 65.332, 70.574
Angle α, β, γ (deg.)90.000, 96.304, 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-842-

HOH

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Components

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


Mass: 43078.855 Da / Num. of mol.: 1 / Mutation: T312K, H333F
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)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
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: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 47815 / % possible obs: 96.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.25
Reflection shellResolution: 1.65→1.75 Å / Num. unique obs: 6664 / CC1/2: 0.991

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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: 1.65→40 Å / SU ML: 0.2716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2131
RfactorNum. reflection% reflection
Rfree0.1944 2389 5 %
Rwork0.1639 --
obs0.1654 47776 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 7 380 3144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562941
X-RAY DIFFRACTIONf_angle_d0.77553981
X-RAY DIFFRACTIONf_chiral_restr0.0516421
X-RAY DIFFRACTIONf_plane_restr0.0054534
X-RAY DIFFRACTIONf_dihedral_angle_d18.29421780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.7007850.67741612X-RAY DIFFRACTION58.9
1.68-1.720.23181400.24082675X-RAY DIFFRACTION97.64
1.72-1.760.20741420.16272692X-RAY DIFFRACTION98.51
1.76-1.80.191450.15632745X-RAY DIFFRACTION98.57
1.8-1.850.17271420.15492695X-RAY DIFFRACTION98.78
1.85-1.910.20471430.15312732X-RAY DIFFRACTION99.21
1.91-1.970.20531430.15352720X-RAY DIFFRACTION98.83
1.97-2.040.18711430.15842717X-RAY DIFFRACTION98.62
2.04-2.120.20081440.15342728X-RAY DIFFRACTION98.76
2.12-2.220.23061440.15362729X-RAY DIFFRACTION99.1
2.22-2.330.17171440.15222749X-RAY DIFFRACTION98.7
2.33-2.480.18551430.1572709X-RAY DIFFRACTION99.41
2.48-2.670.19221460.16432781X-RAY DIFFRACTION99.8
2.67-2.940.20191470.16142784X-RAY DIFFRACTION99.93
2.94-3.370.18881440.15652742X-RAY DIFFRACTION99.9
3.37-4.240.19111470.1412794X-RAY DIFFRACTION99.73
4.24-400.14071470.15312783X-RAY DIFFRACTION97.83

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