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- PDB-6yhd: tRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptoph... -

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Basic information

Entry
Database: PDB / ID: 6yhd
TitletRNA-guanine Transglycosylase (TGT) labeled with 5-fluorotryptophan in co-crystallized complex with 6-amino-4-(2-((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)ethyl)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / HOMODIMER / 19F NMR
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-1WK / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNguyen, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Co-crystallization, nanoESI-MS and 19F NMR 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)43,8176
Polymers43,1421
Non-polymers6755
Water7,458414
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,63412
Polymers86,2842
Non-polymers1,35110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4510 Å2
ΔGint-40 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.579, 65.369, 70.564
Angle α, β, γ (deg.)90.000, 96.129, 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-868-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 419 molecules

#2: Chemical ChemComp-1WK / methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-beta-D-ribo-hexofuranoside


Mass: 390.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.91 %
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: Oct 11, 2019
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: 1.25→22.52 Å / Num. obs: 112100 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.82
Reflection shellResolution: 1.25→1.33 Å / Num. unique obs: 17917 / CC1/2: 0.807

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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: 1.25→22.52 Å / SU ML: 0.0976 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.6937
RfactorNum. reflection% reflection
Rfree0.1438 5604 5 %
Rwork0.1208 --
obs0.122 112074 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→22.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 42 414 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693158
X-RAY DIFFRACTIONf_angle_d0.99694291
X-RAY DIFFRACTIONf_chiral_restr0.0714445
X-RAY DIFFRACTIONf_plane_restr0.0068576
X-RAY DIFFRACTIONf_dihedral_angle_d24.29371179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.24071750.22973332X-RAY DIFFRACTION93.42
1.26-1.280.26781870.22023546X-RAY DIFFRACTION99.76
1.28-1.30.21531850.19983527X-RAY DIFFRACTION99.44
1.3-1.310.21651860.18753535X-RAY DIFFRACTION99.84
1.31-1.330.18991900.183598X-RAY DIFFRACTION99.71
1.33-1.350.19651840.16943498X-RAY DIFFRACTION99.57
1.35-1.370.18211870.1633554X-RAY DIFFRACTION99.65
1.37-1.390.1781870.15663558X-RAY DIFFRACTION99.6
1.39-1.410.16941840.13963499X-RAY DIFFRACTION99.25
1.41-1.430.15951890.13983579X-RAY DIFFRACTION99.63
1.43-1.460.14911860.12863533X-RAY DIFFRACTION99.41
1.46-1.480.14221850.12233525X-RAY DIFFRACTION99.52
1.48-1.510.16991890.11683586X-RAY DIFFRACTION99.55
1.51-1.540.13661850.10693514X-RAY DIFFRACTION99.49
1.54-1.580.15141850.10373516X-RAY DIFFRACTION99.41
1.58-1.610.13071870.09983553X-RAY DIFFRACTION99.42
1.61-1.650.14281870.09963553X-RAY DIFFRACTION99.81
1.65-1.70.13961880.09653564X-RAY DIFFRACTION99.89
1.7-1.750.13011890.09733586X-RAY DIFFRACTION99.87
1.75-1.80.12821870.09873571X-RAY DIFFRACTION99.81
1.8-1.870.1331880.10073557X-RAY DIFFRACTION99.73
1.87-1.940.13121850.10323527X-RAY DIFFRACTION99.73
1.94-2.030.11641880.10473556X-RAY DIFFRACTION99.76
2.03-2.140.12851890.10553605X-RAY DIFFRACTION99.79
2.14-2.270.13181870.1093556X-RAY DIFFRACTION99.65
2.27-2.450.12541880.10793555X-RAY DIFFRACTION99.1
2.45-2.690.121870.11193557X-RAY DIFFRACTION99.05
2.69-3.080.13611870.123566X-RAY DIFFRACTION98.87
3.08-3.880.13911900.12613601X-RAY DIFFRACTION99.84
3.88-22.520.16981930.1383663X-RAY DIFFRACTION99.72

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