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- PDB-4q8v: tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amin... -

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Basic information

Entry
Database: PDB / ID: 4q8v
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzonitrile
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/transferase inhibitor / Guanine Exchange Enzyme / preQ1 / tRNA / 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-2YX / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.396 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Addressing a New Subpocket of TGT by Elongated 2-Amino-lin-benzoguanines
Authors: Neeb, M. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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)43,5734
Polymers43,0701
Non-polymers5033
Water6,936385
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1458
Polymers86,1402
Non-polymers1,0066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5270 Å2
ΔGint-15 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.164, 65.098, 70.760
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-613-

HOH

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Components

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


Mass: 43069.828 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme
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-ZM-WT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2YX / 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzonitrile


Mass: 345.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N7O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: ...AUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288 (1995). THE CORRECT RESIDUE IS A LYS

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013 / Details: Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 79794 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 11
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 12619 / Rsym value: 0.483 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.396→21.823 Å / SU ML: 0.14 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 15.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 3989 5 %Random
Rwork0.1313 ---
obs0.1329 79777 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.396→21.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 33 385 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063025
X-RAY DIFFRACTIONf_angle_d1.0634095
X-RAY DIFFRACTIONf_dihedral_angle_d12.11157
X-RAY DIFFRACTIONf_chiral_restr0.068431
X-RAY DIFFRACTIONf_plane_restr0.005575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3963-1.41330.31451190.27832272X-RAY DIFFRACTION82
1.4133-1.43120.3081440.23032731X-RAY DIFFRACTION100
1.4312-1.450.23741450.21692761X-RAY DIFFRACTION100
1.45-1.46990.24261460.18222758X-RAY DIFFRACTION100
1.4699-1.49080.19511420.16422701X-RAY DIFFRACTION100
1.4908-1.51310.19781480.15242808X-RAY DIFFRACTION100
1.5131-1.53670.18911420.14222710X-RAY DIFFRACTION100
1.5367-1.56190.19721450.13252758X-RAY DIFFRACTION100
1.5619-1.58880.18291450.12732747X-RAY DIFFRACTION100
1.5888-1.61770.15891430.12152720X-RAY DIFFRACTION100
1.6177-1.64880.17231470.12372792X-RAY DIFFRACTION100
1.6488-1.68250.16051440.11942735X-RAY DIFFRACTION100
1.6825-1.7190.16711430.11532725X-RAY DIFFRACTION99
1.719-1.7590.15791460.11172772X-RAY DIFFRACTION99
1.759-1.8030.13771440.10782720X-RAY DIFFRACTION99
1.803-1.85170.16281430.10672728X-RAY DIFFRACTION99
1.8517-1.90620.16281430.10652717X-RAY DIFFRACTION99
1.9062-1.96770.13571440.1112731X-RAY DIFFRACTION99
1.9677-2.03790.14121430.1082717X-RAY DIFFRACTION98
2.0379-2.11950.13391430.11262716X-RAY DIFFRACTION98
2.1195-2.21580.1611420.11312709X-RAY DIFFRACTION98
2.2158-2.33250.1351430.1152712X-RAY DIFFRACTION97
2.3325-2.47850.13581410.12472674X-RAY DIFFRACTION97
2.4785-2.66950.16611420.13632695X-RAY DIFFRACTION97
2.6695-2.93760.1671420.1392707X-RAY DIFFRACTION97
2.9376-3.36140.16611400.1422659X-RAY DIFFRACTION96
3.3614-4.22990.14181400.13142663X-RAY DIFFRACTION95
4.2299-21.82550.17451400.14462650X-RAY DIFFRACTION93

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