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- PDB-4kwo: tRNA guanine transglycosylase (TGT) in complex with Furanoside-Ba... -

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Basic information

Entry
Database: PDB / ID: 4kwo
TitletRNA guanine transglycosylase (TGT) in complex with Furanoside-Based lin-Benzoguanine 3
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE FURANOSIDE-BASED INHIBITOR COMPLEX / Tim Barrel / GLYCOSYLTRANSFERASE / Zinc-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1UD / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: Chemistry / Year: 2015
Title: Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appended lin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT).
Authors: Barandun, L.J. / Ehrmann, F.R. / Zimmerli, D. / Immekus, F. / Giroud, M. / Grunenfelder, C. / Schweizer, W.B. / Bernet, B. / Betz, M. / Heine, A. / Klebe, G. / Diederich, F.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6324
Polymers43,0701
Non-polymers5623
Water5,098283
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2648
Polymers86,1402
Non-polymers1,1246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2540 Å2
ΔGint-22 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 65.047, 71.411
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 43069.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-1UD / methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-3-O-methyl-beta-D-ribo-hexofuranoside


Mass: 404.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N6O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 23, 2013 / Details: RH-COATED SILICON WITH INDIRECT WATER COOLING
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 90020 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.041 / Net I/σ(I): 28
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Num. unique all: 4448 / Rsym value: 0.431 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY 1PUD

1pud


Resolution: 1.32→26 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.71 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 4522 5.02 %random
Rwork0.1464 ---
obs0.1473 90014 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 36 283 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062971
X-RAY DIFFRACTIONf_angle_d1.0724049
X-RAY DIFFRACTIONf_dihedral_angle_d12.6311128
X-RAY DIFFRACTIONf_chiral_restr0.069433
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3330.251360.19852758X-RAY DIFFRACTION94
1.333-1.34870.21431510.18182829X-RAY DIFFRACTION97
1.3487-1.36520.21761400.16482783X-RAY DIFFRACTION98
1.3652-1.38240.15241500.1612817X-RAY DIFFRACTION97
1.3824-1.40060.17141540.15262856X-RAY DIFFRACTION98
1.4006-1.41980.18971330.14682813X-RAY DIFFRACTION98
1.4198-1.44010.16131540.13992836X-RAY DIFFRACTION98
1.4401-1.46160.18291410.1362800X-RAY DIFFRACTION98
1.4616-1.48440.16851610.12832871X-RAY DIFFRACTION98
1.4844-1.50880.17421420.12032819X-RAY DIFFRACTION98
1.5088-1.53480.12761470.11452860X-RAY DIFFRACTION99
1.5348-1.56270.15481600.1092819X-RAY DIFFRACTION98
1.5627-1.59270.13831460.1022851X-RAY DIFFRACTION98
1.5927-1.62520.13841450.10272886X-RAY DIFFRACTION99
1.6252-1.66060.13611460.10592847X-RAY DIFFRACTION99
1.6606-1.69920.13261440.11042871X-RAY DIFFRACTION99
1.6992-1.74170.14111800.11532851X-RAY DIFFRACTION99
1.7417-1.78870.13331190.11792929X-RAY DIFFRACTION99
1.7887-1.84140.12921620.11532833X-RAY DIFFRACTION99
1.8414-1.90080.15181650.1232873X-RAY DIFFRACTION99
1.9008-1.96870.13511600.12792879X-RAY DIFFRACTION99
1.9687-2.04750.14891450.12922877X-RAY DIFFRACTION100
2.0475-2.14060.18091460.12922918X-RAY DIFFRACTION100
2.1406-2.25340.16161590.14132879X-RAY DIFFRACTION100
2.2534-2.39450.17211520.14822903X-RAY DIFFRACTION100
2.3945-2.57930.15661450.15992913X-RAY DIFFRACTION100
2.5793-2.83850.17191530.16362924X-RAY DIFFRACTION100
2.8385-3.24860.18061830.16772891X-RAY DIFFRACTION100
3.2486-4.09030.17611610.15332863X-RAY DIFFRACTION98
4.0903-25.96840.16161420.18592643X-RAY DIFFRACTION89

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