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- PDB-3gc5: tRNA-guanine transglycosylase in complex with 6-amino-4-(2-aminoe... -

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Basic information

Entry
Database: PDB / ID: 3gc5
TitletRNA-guanine transglycosylase in complex with 6-amino-4-(2-aminoethyl)-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / drug design / TIM Barrel / tRNA modification / Glycosyltransferase / Metal-binding / Queuosine biosynthesis / tRNA processing
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-2MQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsRitschel, T. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2009
Title: How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase
Authors: Ritschel, T. / Kohler, P.C. / Neudert, G. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionFeb 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)43,5416
Polymers42,9261
Non-polymers6155
Water5,116284
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,08112
Polymers85,8512
Non-polymers1,23010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3150 Å2
ΔGint-19 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 65.000, 70.800
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1189-

HOH

21A-1275-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt, ZMO0363 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3)
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-2MQ / 6-amino-4-(2-aminoethyl)-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 273.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N7O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Sequence details312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J. ...312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J.Y. ET AL [SUBMITTED (OCT-2000) TO THE EMBL/GENBANK/DDBJ DATABASES]

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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: 2.19 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM TRIS HCl, 1mM DTT, 10% DMSO, 5% PEG 8000, 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 MX225HE / Detector: CCD / Date: Feb 6, 2009 / 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→30 Å / Num. all: 79791 / Num. obs: 79791 / % possible obs: 99.4 % / Redundancy: 3.8 % / Net I/σ(I): 33.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.307 / % possible all: 94.6

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Processing

Software
NameClassification
MxCuBEdata collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→10 Å / Num. parameters: 12899 / Num. restraintsaints: 12278 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 3862 5 %RANDOM
all0.1632 76625 --
obs0.1618 76625 95.6 %-
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 2760 / Occupancy sum non hydrogen: 3146
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 39 284 3144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0267
X-RAY DIFFRACTIONs_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0

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