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- PDB-6yry: tRNA-Guanine Transglycosylase (TGT) H333A mutant crystallised at ... -

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Basic information

Entry
Database: PDB / ID: 6yry
TitletRNA-Guanine Transglycosylase (TGT) H333A 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 ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 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
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3445
Polymers43,0031
Non-polymers3424
Water4,918273
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,68910
Polymers86,0062
Non-polymers6838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4300 Å2
ΔGint-24 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.315, 65.147, 70.891
Angle α, β, γ (deg.)90.000, 96.481, 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-758-

HOH

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Components

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


Mass: 43002.762 Da / Num. of mol.: 1 / Mutation: T312K, H333A
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)
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.: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 48.95 %
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, streak seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Site: BESSY / Beamline: 14.1 / Type: BRUKER IMUS MICROFOCUS / Details: Incoatec microfocus source / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→44.87 Å / Num. obs: 35506 / % possible obs: 97.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.43
Reflection shellResolution: 1.82→1.93 Å / Num. unique obs: 5627 / CC1/2: 0.766

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Processing

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

1pud


Resolution: 1.82→44.87 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2036 1773 5 %
Rwork0.1754 33687 -
obs0.1768 35460 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.56 Å2
Refinement stepCycle: LAST / Resolution: 1.82→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 19 274 3026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062863
X-RAY DIFFRACTIONf_angle_d0.77863865
X-RAY DIFFRACTIONf_chiral_restr0.0505412
X-RAY DIFFRACTIONf_plane_restr0.0059515
X-RAY DIFFRACTIONf_dihedral_angle_d18.03191724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.3251320.27882509X-RAY DIFFRACTION94.69
1.87-1.930.2721360.23872584X-RAY DIFFRACTION96.83
1.93-1.990.26751350.22832558X-RAY DIFFRACTION96.28
1.99-2.060.2491360.19762575X-RAY DIFFRACTION96.89
2.06-2.140.23471370.18822611X-RAY DIFFRACTION97.24
2.14-2.240.21071380.17592610X-RAY DIFFRACTION98.53
2.24-2.360.21251370.17542608X-RAY DIFFRACTION99.24
2.36-2.510.18891410.16932674X-RAY DIFFRACTION99.58
2.51-2.70.23451390.17762642X-RAY DIFFRACTION99.18
2.7-2.970.19881380.17342620X-RAY DIFFRACTION98.04
2.97-3.40.18561370.16452598X-RAY DIFFRACTION97.12
3.4-4.290.1561370.15092606X-RAY DIFFRACTION96.01
4.29-44.870.20421300.16822492X-RAY DIFFRACTION90.82

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