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

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Basic information

Entry
Database: PDB / ID: 4leq
TitletRNA guanine transglycosylase (TGT) in complex with Furanoside-Based lin-Benzoguanine 1
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Tim Barrel / GLYCOSYLTRANSFERASE / Zinc-BINDING / TRANSFERASE / 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-1WK / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas Mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.405 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
DepositionJun 26, 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7456
Polymers43,0701
Non-polymers6755
Water7,710428
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49112
Polymers86,1402
Non-polymers1,35110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3240 Å2
ΔGint-17 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.623, 65.106, 70.357
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-855-

HOH

21A-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: 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

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Non-polymers , 5 types, 433 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
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
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: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 8, 2012 / 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: 1.405→50 Å / Num. all: 76331 / Num. obs: 76331 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 1.405→1.43 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3734 / Rsym value: 0.497 / % possible all: 94.7

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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: PDB ENTRY 1PUD

1pud


Resolution: 1.405→40.876 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1485 3838 5.03 %random
Rwork0.1232 ---
obs0.1245 76328 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.405→40.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 42 428 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063110
X-RAY DIFFRACTIONf_angle_d1.1064220
X-RAY DIFFRACTIONf_dihedral_angle_d12.8561193
X-RAY DIFFRACTIONf_chiral_restr0.07446
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.405-1.42240.19671070.16752250X-RAY DIFFRACTION81
1.4224-1.44110.20911400.15322641X-RAY DIFFRACTION95
1.4411-1.46090.15511470.142631X-RAY DIFFRACTION95
1.4609-1.48170.18321290.13022665X-RAY DIFFRACTION95
1.4817-1.50390.15931280.12642655X-RAY DIFFRACTION95
1.5039-1.52740.1691400.11622622X-RAY DIFFRACTION95
1.5274-1.55240.14721340.11242671X-RAY DIFFRACTION96
1.5524-1.57920.16381400.10762625X-RAY DIFFRACTION96
1.5792-1.60790.15281360.10142667X-RAY DIFFRACTION96
1.6079-1.63880.13231380.10222700X-RAY DIFFRACTION96
1.6388-1.67230.13461430.09872663X-RAY DIFFRACTION96
1.6723-1.70860.13191340.09982719X-RAY DIFFRACTION97
1.7086-1.74840.14621520.10072673X-RAY DIFFRACTION97
1.7484-1.79210.15471560.10912665X-RAY DIFFRACTION97
1.7921-1.84060.13181400.10312686X-RAY DIFFRACTION97
1.8406-1.89470.14751410.1062686X-RAY DIFFRACTION97
1.8947-1.95590.14281510.10752725X-RAY DIFFRACTION97
1.9559-2.02580.14681400.1092707X-RAY DIFFRACTION98
2.0258-2.10690.12661440.10782719X-RAY DIFFRACTION98
2.1069-2.20280.14541560.1142715X-RAY DIFFRACTION98
2.2028-2.31890.13371530.11882747X-RAY DIFFRACTION98
2.3189-2.46420.17231590.12672712X-RAY DIFFRACTION98
2.4642-2.65440.13851580.13572744X-RAY DIFFRACTION98
2.6544-2.92140.16011270.13462800X-RAY DIFFRACTION99
2.9214-3.3440.15011400.13652770X-RAY DIFFRACTION99
3.344-4.21240.13371430.12672797X-RAY DIFFRACTION99
4.2124-40.89330.15791620.14482835X-RAY DIFFRACTION99

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