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- PDB-2nqz: Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaz... -

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Basic information

Entry
Database: PDB / ID: 2nqz
TitleTrna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / preQ1
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
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
7-DEAZA-7-AMINOMETHYL-GUANINE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsTidten, N. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Plos One / Year: 2013
Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor
Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE See Ref. 1 and 2 in the sequence database, TGT_ZYMMO.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5469
Polymers42,7481
Non-polymers7978
Water4,648258
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,09118
Polymers85,4972
Non-polymers1,59416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.900, 64.930, 71.180
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1296-

HOH

21A-1329-

HOH

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Components

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


Mass: 42748.418 Da / Num. of mol.: 1 / Mutation: Y106F, C158V, A232S, V233G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET-9d / 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-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSee Ref. 1 and 2 in the sequence database, TGT_ZYMMO.

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, 14mg/ml TGT, 20mM preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 16, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.46→20 Å / Num. all: 64991 / Num. obs: 64991 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rsym value: 0.044 / Net I/σ(I): 18

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y5X

1y5x


Resolution: 1.46→8 Å / Num. parameters: 31725 / Num. restraintsaints: 39887 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 38064 5 %RANDOM
Rwork0.15 ---
all0.1515 64991 --
obs0.15 64991 92.3 %-
Solvent computationSolvent model: BABINET (SWAT)
Refine analyzeNum. disordered residues: 31 / Occupancy sum hydrogen: 2827 / Occupancy sum non hydrogen: 3365
Refinement stepCycle: LAST / Resolution: 1.46→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 50 258 3047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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