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- PDB-6ygr: tRNA-guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 6ygr
TitletRNA-guanine Transglycosylase (TGT) in co-crystallized complex with 6-Amino-4-(2-phenylethyl)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / HOMODIMER
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
Chem-NE8 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization and nanoESI-MS reveal dimer disturbing inhibitors and conformational changes at dimer contacts
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: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 ..._atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5 / _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)43,4413
Polymers43,0701
Non-polymers3712
Water3,873215
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8816
Polymers86,1402
Non-polymers7414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)83.921, 65.022, 71.104
Angle α, β, γ (deg.)90.000, 93.943, 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: 43069.828 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)
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: Chemical ChemComp-NE8 / 6-AMINO-4-(2-PHENYLETHYL)-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE


Mass: 305.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.26 %
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 12, 2018
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: 1.7→41.86 Å / Num. obs: 40707 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.31
Reflection shellResolution: 1.7→1.81 Å / Num. unique obs: 6285 / CC1/2: 0.802

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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: 1.7→41.86 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2283
RfactorNum. reflection% reflection
Rfree0.2207 2036 5 %
Rwork0.1821 --
obs0.184 40699 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 24 215 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562785
X-RAY DIFFRACTIONf_angle_d0.78013770
X-RAY DIFFRACTIONf_chiral_restr0.0493397
X-RAY DIFFRACTIONf_plane_restr0.0052530
X-RAY DIFFRACTIONf_dihedral_angle_d16.45311672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.30771200.28212266X-RAY DIFFRACTION85.67
1.74-1.790.31681360.25292590X-RAY DIFFRACTION98.98
1.79-1.840.28991380.23292618X-RAY DIFFRACTION98.5
1.84-1.890.29891350.22552570X-RAY DIFFRACTION98.11
1.89-1.950.26291330.20722518X-RAY DIFFRACTION96.12
1.95-2.020.20841370.18852609X-RAY DIFFRACTION99.53
2.02-2.10.24451380.18592629X-RAY DIFFRACTION98.96
2.1-2.20.20731370.17862598X-RAY DIFFRACTION99.38
2.2-2.310.21551380.1792620X-RAY DIFFRACTION98.57
2.31-2.460.22351370.17472599X-RAY DIFFRACTION98.88
2.46-2.650.20211380.18352620X-RAY DIFFRACTION98.39
2.65-2.910.21381330.18742528X-RAY DIFFRACTION96.17
2.91-3.340.22671380.18372635X-RAY DIFFRACTION98.86
3.34-4.20.20281380.15992618X-RAY DIFFRACTION98.36
4.2-41.860.19941400.16722645X-RAY DIFFRACTION97.28
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.571672264056-0.2587709074170.02343610042390.348975886520.2679881276970.9160190324910.02568951292540.116533942189-0.00928222016317-0.0178139456107-0.0259488896970.00970432128065-0.00785908085567-0.0649786667989-1.6945560325E-50.1664279527240.0135999856988-0.01786317781770.1291528526820.007146419622150.17371945902194.91440434542.7775272873120.0932529606
20.666013732455-0.1377747366820.6099935086360.168131720151-0.131636224050.69021961165-0.0912793032971-0.04881070617140.0587418211324-0.1487726889750.00469677370617-0.0948280958665-0.35046379425-0.188971829648-0.0001342838969230.2056300454410.0332879268488-0.02305450957810.189084509505-0.00698544091920.17338309720587.117809765515.743471990525.6574261127
30.9549240327680.0385661536449-0.2503327445171.220972161330.2966176918451.012021517190.0174999574779-0.1137081173910.02521314259990.02807035089020.0273461432515-0.117090102704-0.1299169346060.106791328895-5.87748138405E-50.1544720617820.0058704171737-0.01816352700290.131600750777-0.006606557521940.14616207568104.91320203712.902925887927.1377742204
4-0.168561516431-0.02719293544620.142760624068-0.0831981422302-0.04110328830840.178083619399-0.0945893177511-0.04290509590570.08339952947860.04464282211290.0787715190491-0.00328837459576-0.275879830271-0.1828572995832.39725209974E-50.2120753295050.00400783734168-0.02230170820870.1998585981470.03281889819790.189928425165100.72648732812.24147581031.72877315143
50.6067691100630.193879797089-0.03551800272630.2167919324440.1616302778780.4396325314730.04348833085290.1266804019160.004850168548010.04302839644770.130090123267-0.2630452955180.279472375690.3196720570030.002934671163120.3387995910030.00897631647626-0.06889757481310.180882682412-0.01101508561230.22561154030494.23515107458.41276521425-10.1256581419
60.2392573376390.01584310050260.2279835903580.192264333111-0.2318038526140.4095370487510.08164329710110.197530726194-0.0661821167155-0.198372282217-0.0332327260052-0.03441054351540.1079358747250.06547317457940.04266495253940.1560913998540.02889524447630.02066282162550.199052361695-0.0001288026314830.143864627687105.4854125323.179268418614.00802048063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 307 )
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 339 )
6X-RAY DIFFRACTION6chain 'A' and (resid 340 through 383 )

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