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- PDB-3gc4: tRNA-guanine transglycosylase in complex with inhibitor -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3gc4
TitletRNA-guanine transglycosylase in complex with inhibitor
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-AAQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.8 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 1.2Nov 1, 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 / 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)43,8158
Polymers42,9261
Non-polymers8897
Water3,801211
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,63016
Polymers85,8512
Non-polymers1,77914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-17 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.500, 64.900, 70.400
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121

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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-AAQ / 6-amino-4-[2-(benzylamino)ethyl]-2-(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 363.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N7O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2008 / Details: mirror
RadiationMonochromator: Yale Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 36099 / Num. obs: 36099 / % possible obs: 95.6 % / Redundancy: 3.8 % / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.25 / % possible all: 65.6

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Processing

Software
NameClassification
CrystalCleardata collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1P0E

1p0e


Resolution: 1.8→10 Å / Num. parameters: 12094 / Num. restraintsaints: 11663 / 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
Rfree0.1989 1713 5 %RANDOM
all0.1611 34502 --
obs0.1599 34502 91.9 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 2659 / Occupancy sum non hydrogen: 2979
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 58 211 2978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0239
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0

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