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- PDB-6ygz: tRNA Guanine Transglycosylase (TGT) labelled with 5-fluoro-trypto... -

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Basic information

Entry
Database: PDB / ID: 6ygz
TitletRNA Guanine Transglycosylase (TGT) labelled with 5-fluoro-tryptophan 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 / HOMODIMER / 19F NMR / TRNA / TGT
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: 1.86 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
DepositionMar 28, 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5133
Polymers43,1421
Non-polymers3712
Water3,063170
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0256
Polymers86,2842
Non-polymers7414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3530 Å2
ΔGint-28 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.800, 64.904, 71.299
Angle α, β, γ (deg.)90.000, 94.135, 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: 43141.789 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.: 170 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
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: May 17, 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: 1.86→35.56 Å / Num. obs: 31999 / % possible obs: 94.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.51 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.34
Reflection shellResolution: 1.86→1.97 Å / Num. unique obs: 5260 / CC1/2: 0.898

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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: 1.86→35.56 Å / SU ML: 0.3019 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.2888
RfactorNum. reflection% reflection
Rfree0.2483 1517 5 %
Rwork0.2134 --
obs0.2152 30350 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.37 Å2
Refinement stepCycle: LAST / Resolution: 1.86→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 24 170 2842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642761
X-RAY DIFFRACTIONf_angle_d0.86143739
X-RAY DIFFRACTIONf_chiral_restr0.0516392
X-RAY DIFFRACTIONf_plane_restr0.006526
X-RAY DIFFRACTIONf_dihedral_angle_d14.90661648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.920.57861120.57812139X-RAY DIFFRACTION76.75
1.92-1.990.3181220.35222328X-RAY DIFFRACTION82.85
1.99-2.070.45431390.34012647X-RAY DIFFRACTION94.28
2.07-2.160.31981360.27862583X-RAY DIFFRACTION92.04
2.16-2.270.3791260.32752387X-RAY DIFFRACTION85.86
2.27-2.420.22011490.18522827X-RAY DIFFRACTION99.83
2.42-2.60.23341470.18742792X-RAY DIFFRACTION99.86
2.6-2.870.23921470.19192804X-RAY DIFFRACTION99.26
2.87-3.280.2281470.18232798X-RAY DIFFRACTION99.23
3.28-4.130.18711420.1692688X-RAY DIFFRACTION94.52
4.13-35.560.19631500.16792840X-RAY DIFFRACTION98.45
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)
10.0929602468226-0.04339449082440.03244220270950.0895364665137-0.1657554278390.173167747406-0.0415561765235-0.0495317025263-0.1336585754940.1387205305690.05396412365960.05246288117250.3168226824010.0293549598664-9.88199032591E-70.2273166822390.0162062270408-0.00415806808840.191156108424-0.01337827181980.240458494411101.982319576-4.1401120192422.2908932577
20.267799209516-0.002943401293130.3146384099470.08670480195930.02235559077370.286970450618-0.06032916328560.05048513597370.0930539307786-0.00121512890906-0.00738636567952-0.0466202208822-0.0198526037037-0.163988246107-5.11425270386E-50.148021222140.0251808008689-0.02251266580540.1782557294280.007945743105650.14699055992486.73223790979.9338951517918.8358648647
30.3056265404030.1074460161860.06059651178450.4006103266160.08460880869630.26478398811-0.06188942099820.01045598192940.038462034716-0.2870072164520.141207029357-0.206383938389-0.28682600711-0.1989209504040.02994896464840.2952217060010.0505625787903-0.04293844175990.16729480196-0.01288009991090.26463065810691.663977744715.44849523521.6122761657
40.33198057754-0.2606275034830.1766115059321.018822564950.4965346175041.152495402710.00907588705206-0.1267832276350.0254542844061-0.01492161920410.034086697939-0.097612598187-0.1658921540260.0560825789453-0.000448900325230.1794845940550.0105577134452-0.001838575291940.164742735293-0.009951472502820.171046688998103.38991463814.113948914727.8716889365
5-0.006850126104620.04832749584420.2128548577340.00723916724341-0.1559980433340.354006682317-0.0301329870751-0.04198455217160.06677748551610.156670449170.2370788956280.180877849547-0.557669360729-0.1801294740730.006179209691930.2409575160270.00159635508048-0.01856494015180.213686425090.04044155739760.226097007223101.62952928612.2821454383.28718119259
60.3190369072350.1373986445580.04720692330950.1552977034190.1338477183750.1321543884020.03066637877170.11225435228-0.0257403488208-0.2565810665780.0124917583196-0.1989745217440.1924960859160.1835825352578.2370671149E-50.2508760743140.0038348603426-0.002175917082820.212827944370.006924978683610.21638485111795.82674369098.92781061438-10.2943793133
70.2756877883980.2257741599520.1293692392290.096614892996-0.08753266237630.325374057580.1159332811240.383027739433-0.0859905795268-0.116371286565-0.0319688570267-0.06646201986170.01008149057160.04375822544840.05365907503250.1824359949390.04170810761950.0381624518780.2410544492810.01521532138170.182621602082106.5191101163.285158224224.18638319844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 304 )
6X-RAY DIFFRACTION6chain 'A' and (resid 305 through 339 )
7X-RAY DIFFRACTION7chain 'A' and (resid 340 through 383 )

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