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- PDB-4q4o: tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2... -

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Basic information

Entry
Database: PDB / ID: 4q4o
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2-(piperidin-1-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-2YM / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
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 / pdbx_struct_special_symmetry / 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)43,6167
Polymers42,9261
Non-polymers6916
Water7,008389
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,23314
Polymers85,8512
Non-polymers1,38112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area5010 Å2
ΔGint-37 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.823, 64.696, 70.711
Angle α, β, γ (deg.)90.00, 93.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-600-

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: 42925.703 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: pET9d-ZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 395 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-2YM / 6-amino-2-{[2-(piperidin-1-yl)ethyl]amino}-3,5-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 327.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N7O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.51 %
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: 1.35→30 Å / Num. obs: 87189 / % possible obs: 98.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.046 / Net I/σ(I): 15.4
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 4254 / Rsym value: 0.388 / % possible all: 98.3

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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: 1PUD

1pud


Resolution: 1.35→27.133 Å / SU ML: 0.13 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 4379 5.02 %Random
Rwork0.1367 ---
obs0.138 87159 98.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→27.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 42 389 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063046
X-RAY DIFFRACTIONf_angle_d1.0974133
X-RAY DIFFRACTIONf_dihedral_angle_d12.3371175
X-RAY DIFFRACTIONf_chiral_restr0.069436
X-RAY DIFFRACTIONf_plane_restr0.006568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3505-1.36580.29221380.24532427X-RAY DIFFRACTION89
1.3658-1.38190.26821600.2282754X-RAY DIFFRACTION99
1.3819-1.39870.21581580.20482689X-RAY DIFFRACTION98
1.3987-1.41640.24141630.19422773X-RAY DIFFRACTION99
1.4164-1.43510.21991460.17932738X-RAY DIFFRACTION98
1.4351-1.45470.18491420.17132753X-RAY DIFFRACTION99
1.4547-1.47550.20461430.14522725X-RAY DIFFRACTION98
1.4755-1.49750.19621550.13522773X-RAY DIFFRACTION99
1.4975-1.52090.16071200.12812767X-RAY DIFFRACTION99
1.5209-1.54590.16321360.12492821X-RAY DIFFRACTION99
1.5459-1.57250.15011430.11312775X-RAY DIFFRACTION100
1.5725-1.60110.13761370.1092795X-RAY DIFFRACTION100
1.6011-1.63190.16651340.11022828X-RAY DIFFRACTION100
1.6319-1.66520.14871510.1082764X-RAY DIFFRACTION100
1.6652-1.70140.161340.11072793X-RAY DIFFRACTION100
1.7014-1.7410.16431700.11272783X-RAY DIFFRACTION100
1.741-1.78450.13861320.11022846X-RAY DIFFRACTION100
1.7845-1.83270.16331430.11042793X-RAY DIFFRACTION100
1.8327-1.88670.14591520.11242739X-RAY DIFFRACTION100
1.8867-1.94750.14391550.10932815X-RAY DIFFRACTION100
1.9475-2.01710.14061630.1112771X-RAY DIFFRACTION100
2.0171-2.09790.1471510.11582784X-RAY DIFFRACTION100
2.0979-2.19330.14361220.11912801X-RAY DIFFRACTION99
2.1933-2.30890.141420.12582835X-RAY DIFFRACTION99
2.3089-2.45350.16711350.13092746X-RAY DIFFRACTION99
2.4535-2.64270.15781610.15282784X-RAY DIFFRACTION99
2.6427-2.90840.15871410.15262794X-RAY DIFFRACTION99
2.9084-3.32860.1631540.14842731X-RAY DIFFRACTION98
3.3286-4.19120.15161380.1392783X-RAY DIFFRACTION97
4.1912-27.1380.17351600.1572600X-RAY DIFFRACTION91

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