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- PDB-4q4r: tRNA-Guanine Transglycosylase (TGT) in Complex with 2-{[2-(Morpho... -

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Basic information

Entry
Database: PDB / ID: 4q4r
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 2-{[2-(Morpholin-4-yl)ethyl]amino}-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / preQ1 / tRNA / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
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-SQO / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.448 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Beyond Affinity: Enthalpy-Entropy Factorization Unravels Complexity of a Flat Structure-Activity Relationship for Inhibition of a tRNA-Modifying Enzyme.
Authors: Neeb, M. / Betz, M. / Heine, A. / Barandun, L.J. / Hohn, C. / Diederich, F. / Klebe, G.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJul 9, 2014ID: 3V0Y
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: 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_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_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)43,5826
Polymers42,9261
Non-polymers6565
Water5,080282
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16312
Polymers85,8512
Non-polymers1,31210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area4690 Å2
ΔGint-16 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.941, 64.837, 70.756
Angle α, β, γ (deg.)90.00, 93.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

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Components

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


Mass: 42925.703 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: pET9d-ZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SQO / 2-{[2-(4-Morpholinyl)ethyl]amino}-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 314.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; ...AUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995).

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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: 2.4 Å3/Da / Density % sol: 48.74 %
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: Apr 4, 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: 1.45→30 Å / Num. obs: 71426 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3566 / Rsym value: 0.465 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.448→29.765 Å / SU ML: 0.14 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 3607 5.05 %Random
Rwork0.136 ---
obs0.1378 71401 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.448→29.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 42 282 3121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052981
X-RAY DIFFRACTIONf_angle_d1.0454036
X-RAY DIFFRACTIONf_dihedral_angle_d12.1181142
X-RAY DIFFRACTIONf_chiral_restr0.068426
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4482-1.46730.26591020.2052163X-RAY DIFFRACTION82
1.4673-1.48740.24171400.18092601X-RAY DIFFRACTION100
1.4874-1.50860.25321350.16172652X-RAY DIFFRACTION100
1.5086-1.53110.20171420.14972606X-RAY DIFFRACTION100
1.5311-1.55510.17051490.13112615X-RAY DIFFRACTION100
1.5551-1.58050.18541240.1262656X-RAY DIFFRACTION100
1.5805-1.60780.18231360.12052612X-RAY DIFFRACTION100
1.6078-1.6370.18161180.11632656X-RAY DIFFRACTION100
1.637-1.66850.17011520.11342607X-RAY DIFFRACTION100
1.6685-1.70260.18031290.11262611X-RAY DIFFRACTION100
1.7026-1.73960.17371480.10942638X-RAY DIFFRACTION100
1.7396-1.780.16261420.10842628X-RAY DIFFRACTION100
1.78-1.82460.16091310.11182620X-RAY DIFFRACTION100
1.8246-1.87390.16861460.12122654X-RAY DIFFRACTION100
1.8739-1.9290.1671370.11562618X-RAY DIFFRACTION100
1.929-1.99130.15331360.1142653X-RAY DIFFRACTION100
1.9913-2.06240.14061430.11892624X-RAY DIFFRACTION100
2.0624-2.1450.1491190.1162669X-RAY DIFFRACTION100
2.145-2.24260.16771490.12532616X-RAY DIFFRACTION100
2.2426-2.36070.15471480.13062609X-RAY DIFFRACTION100
2.3607-2.50860.16931650.14172616X-RAY DIFFRACTION100
2.5086-2.70220.19021360.14572634X-RAY DIFFRACTION99
2.7022-2.97390.17911500.14342607X-RAY DIFFRACTION99
2.9739-3.40370.15831640.14442625X-RAY DIFFRACTION99
3.4037-4.28620.17681240.13612645X-RAY DIFFRACTION99
4.2862-29.77140.17991420.16042559X-RAY DIFFRACTION94

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