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- PDB-2nso: Trna-gunanine-transglycosylase (TGT) mutant Y106F, C158V, A232S, ... -

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Basic information

Entry
Database: PDB / ID: 2nso
TitleTrna-gunanine-transglycosylase (TGT) mutant Y106F, C158V, A232S, V233G- APO-Structure
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TRNA-GUNANINE-TRANSGLYCOSYLASE (TGT)
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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 UNIPROT SEQUENCE DATABASE, TGT_ZYMMO.

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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)43,1294
Polymers42,8801
Non-polymers2503
Water3,333185
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2588
Polymers85,7592
Non-polymers4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 64.830, 70.810
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

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


Mass: 42879.613 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growpH: 8.5
Details: 100 mM Tris/HCl, 1 mM DTT, 5% PEG 8000, 10% DMSO, pH 8.50

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 53101 / % possible obs: 98.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.1331 / Rsym value: 0.071 / Net I/σ(I): 15

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y5X

1y5x


Resolution: 1.6→28.42 Å / Num. parameters: 29645 / Num. restraintsaints: 36523 / 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 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF).
RfactorNum. reflection% reflectionSelection details
Rfree0.221 -5 %RANDOM
Rwork0.162 ---
all0.1644 ---
obs-51779 98.6 %-
Solvent computationSolvent model: BABINET (SWAT)
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 2815 / Occupancy sum non hydrogen: 3240.5
Refinement stepCycle: LAST / Resolution: 1.6→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 13 185 2969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.077

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