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- PDB-3c2y: tRNA-Guanine Transglycosylase (TGT) in complex with 6-Amino-2-met... -

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Basic information

Entry
Database: PDB / ID: 3c2y
TitletRNA-Guanine Transglycosylase (TGT) in complex with 6-Amino-2-methyl-1,7-dihydro-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TIM Barrel / 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-S60 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.78 Å
AuthorsRitschel, T. / Heine, A. / Klebe, G.
CitationJournal: Chembiochem / Year: 2009
Title: Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT
Authors: Ritschel, T. / Hoertner, S. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionJan 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 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)43,6678
Polymers42,9261
Non-polymers7417
Water4,936274
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33416
Polymers85,8512
Non-polymers1,48214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5350 Å2
ΔGint-17 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.300, 64.800, 70.300
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1244-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / 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-S60 / 6-amino-2-methyl-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 2-methyl-lin-Benzoguanine


Mass: 215.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N5O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A MISTAKE IN SWISSPROT FOR P28720. THIS IS REFERRED IN THE ORIGINAL PAPER; REUTER K.K.H., ...THERE IS A MISTAKE IN SWISSPROT FOR P28720. THIS IS REFERRED IN THE ORIGINAL PAPER; REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995). THE CORRECT RESIDUE AT THE POSITION IS 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: 2.2 Å3/Da / Density % sol: 44.1 %
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: Dec 12, 2006 / Details: MIRRORS
RadiationMonochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 36907 / Num. obs: 36907 / % possible obs: 95 % / Redundancy: 1.9 % / Rsym value: 0.055 / Net I/σ(I): 15
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1780 / Rsym value: 0.37 / % possible all: 92.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1P0D

1p0d


Resolution: 1.78→10 Å / Num. parameters: 12544 / Num. restraintsaints: 11778 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1760 -RANDOM
Rwork0.1622 ---
obs0.1641 35094 91.1 %-
all-35094 --
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 2724 / Occupancy sum non hydrogen: 3109.5
Refinement stepCycle: LAST / Resolution: 1.78→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 47 274 3109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0246
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0

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