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- PDB-6yiq: tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex (P... -

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Basic information

Entry
Database: PDB / ID: 6yiq
TitletRNA-Guanine Transglycosylase (TGT) in co-crystallized complex (P2) with 6-amino-2-(methylamino)-4-phenethyl-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-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
Chem-OQN / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization, 19F NMR and nanoESI-MS reveal dimer disturbing inhibitors and conformational changes at dimer contacts
Authors: Nguyen, A. / Heine, A. / Klebe, G.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
B: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2169
Polymers86,1402
Non-polymers1,0767
Water9,692538
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1238
Polymers86,1402
Non-polymers9846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: Queuine tRNA-ribosyltransferase
hetero molecules

B: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30810
Polymers86,1402
Non-polymers1,1688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)70.959, 64.877, 87.456
Angle α, β, γ (deg.)90.000, 94.993, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALA(chain 'A' and (resid 11 through 20 or resid 22...AA11 - 1913 - 21
12GLUGLULYSLYS(chain 'A' and (resid 11 through 20 or resid 22...AA22 - 3324 - 35
13GLYGLYVALVAL(chain 'A' and (resid 11 through 20 or resid 22...AA35 - 5137 - 53
14GLYGLYLEULEU(chain 'A' and (resid 11 through 20 or resid 22...AA63 - 7465 - 76
15LEULEUGLYGLY(chain 'A' and (resid 11 through 20 or resid 22...AA76 - 7978 - 81
16ARGARGMETMET(chain 'A' and (resid 11 through 20 or resid 22...AA82 - 10984 - 111
17THRTHRLYSLYS(chain 'A' and (resid 11 through 20 or resid 22...AA115 - 125117 - 127
18ARGARGILEILE(chain 'A' and (resid 11 through 20 or resid 22...AA132 - 141134 - 143
19ILEILEPROPRO(chain 'A' and (resid 11 through 20 or resid 22...AA143 - 165145 - 167
110ARGARGSERSER(chain 'A' and (resid 11 through 20 or resid 22...AA167 - 170169 - 172
111METMETASPASP(chain 'A' and (resid 11 through 20 or resid 22...AA172 - 187174 - 189
112ARGARGGLUGLU(chain 'A' and (resid 11 through 20 or resid 22...AA189 - 239191 - 241
113PHEPHEPROPRO(chain 'A' and (resid 11 through 20 or resid 22...AA241 - 265243 - 267
114ASPASPASPASP(chain 'A' and (resid 11 through 20 or resid 22...AA267 - 280269 - 282
115VALVALPROPRO(chain 'A' and (resid 11 through 20 or resid 22...AA282 - 284284 - 286
116SERSERILEILE(chain 'A' and (resid 11 through 20 or resid 22...AA287 - 302289 - 304
117ASNASNGLYGLY(chain 'A' and (resid 11 through 20 or resid 22...AA304 - 342306 - 344
118LEULEUILEILE(chain 'A' and (resid 11 through 20 or resid 22...AA345 - 365347 - 367
119GLUGLUPHEPHE(chain 'A' and (resid 11 through 20 or resid 22...AA367 - 382369 - 384
220ARGARGALAALA(chain 'B' and (resid 11 through 16 or (resid 17...BB11 - 1913 - 21
221GLUGLULYSLYS(chain 'B' and (resid 11 through 16 or (resid 17...BB22 - 3324 - 35
222GLYGLYVALVAL(chain 'B' and (resid 11 through 16 or (resid 17...BB35 - 5137 - 53
223GLYGLYLEULEU(chain 'B' and (resid 11 through 16 or (resid 17...BB63 - 7465 - 76
224LEULEUGLYGLY(chain 'B' and (resid 11 through 16 or (resid 17...BB76 - 7978 - 81
225ARGARGMETMET(chain 'B' and (resid 11 through 16 or (resid 17...BB82 - 10984 - 111
226THRTHRLYSLYS(chain 'B' and (resid 11 through 16 or (resid 17...BB115 - 125117 - 127
227ARGARGILEILE(chain 'B' and (resid 11 through 16 or (resid 17...BB132 - 141134 - 143
228ILEILEPROPRO(chain 'B' and (resid 11 through 16 or (resid 17...BB143 - 165145 - 167
229ARGARGSERSER(chain 'B' and (resid 11 through 16 or (resid 17...BB167 - 170169 - 172
230METMETASPASP(chain 'B' and (resid 11 through 16 or (resid 17...BB172 - 187174 - 189
231ARGARGGLUGLU(chain 'B' and (resid 11 through 16 or (resid 17...BB189 - 239191 - 241
232PHEPHEPROPRO(chain 'B' and (resid 11 through 16 or (resid 17...BB241 - 265243 - 267
233ASPASPASPASP(chain 'B' and (resid 11 through 16 or (resid 17...BB267 - 280269 - 282
234VALVALPROPRO(chain 'B' and (resid 11 through 16 or (resid 17...BB282 - 284284 - 286
235SERSERILEILE(chain 'B' and (resid 11 through 16 or (resid 17...BB287 - 302289 - 304
236ASNASNGLYGLY(chain 'B' and (resid 11 through 16 or (resid 17...BB304 - 342306 - 344
237LEULEUILEILE(chain 'B' and (resid 11 through 16 or (resid 17...BB345 - 365347 - 367
238GLUGLUPHEPHE(chain 'B' and (resid 11 through 16 or (resid 17...BB367 - 382369 - 384

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Components

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


Mass: 43069.828 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-OQN / 6-amino-2-(methylamino)-4-phenethyl-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 6-azanyl-2-(methylamino)-4-(2-phenylethyl)-3,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 334.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
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: Mar 3, 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: 1.58→43.56 Å / Num. obs: 105940 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.21
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 16991 / CC1/2: 0.837

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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: 1.58→43.56 Å / SU ML: 0.1541 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.8431
RfactorNum. reflection% reflection
Rfree0.2019 5275 5 %
Rwork0.1597 --
obs0.1618 105519 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.32 Å2
Refinement stepCycle: LAST / Resolution: 1.58→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 70 538 6047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825788
X-RAY DIFFRACTIONf_angle_d0.93197842
X-RAY DIFFRACTIONf_chiral_restr0.0522823
X-RAY DIFFRACTIONf_plane_restr0.00641107
X-RAY DIFFRACTIONf_dihedral_angle_d17.48823485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.590.31351600.22373041X-RAY DIFFRACTION90.09
1.59-1.610.24661800.20353431X-RAY DIFFRACTION98.99
1.61-1.630.30071780.19143384X-RAY DIFFRACTION98.67
1.63-1.650.23761820.18043439X-RAY DIFFRACTION99.04
1.65-1.680.22121760.16613360X-RAY DIFFRACTION98.85
1.68-1.70.23861790.17023397X-RAY DIFFRACTION98.73
1.7-1.720.25011760.17983355X-RAY DIFFRACTION97.54
1.72-1.750.20021780.16133377X-RAY DIFFRACTION98.07
1.75-1.780.21671760.14833361X-RAY DIFFRACTION98
1.78-1.80.20051790.14373383X-RAY DIFFRACTION98.18
1.8-1.840.20721800.1443420X-RAY DIFFRACTION99.42
1.84-1.870.23181800.16523422X-RAY DIFFRACTION99.26
1.87-1.910.25881710.20943255X-RAY DIFFRACTION94.35
1.91-1.940.32661590.24263016X-RAY DIFFRACTION87.73
1.94-1.990.191780.15543379X-RAY DIFFRACTION98.04
1.99-2.030.16761810.13763449X-RAY DIFFRACTION98.72
2.03-2.080.23921610.17263061X-RAY DIFFRACTION88.96
2.08-2.140.18491750.13983321X-RAY DIFFRACTION97.03
2.14-2.20.16861780.13973372X-RAY DIFFRACTION98.34
2.2-2.270.21741640.17453118X-RAY DIFFRACTION90.07
2.27-2.350.20111790.13983417X-RAY DIFFRACTION98.9
2.35-2.450.19121800.13863406X-RAY DIFFRACTION98.76
2.45-2.560.17771800.13453429X-RAY DIFFRACTION98.63
2.56-2.70.20281730.14723285X-RAY DIFFRACTION94.9
2.7-2.860.16841760.14923353X-RAY DIFFRACTION96.58
2.86-3.090.21041800.14983434X-RAY DIFFRACTION98.5
3.09-3.40.1871800.15033423X-RAY DIFFRACTION98.74
3.4-3.890.18621720.14543287X-RAY DIFFRACTION94.48
3.89-4.90.16231790.1443388X-RAY DIFFRACTION96.51
4.9-43.560.22731850.21583481X-RAY DIFFRACTION96.88

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