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- PDB-3bld: tRNA guanine transglycosylase V233G mutant preQ1 complex structure -

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Basic information

Entry
Database: PDB / ID: 3bld
TitletRNA guanine transglycosylase V233G mutant preQ1 complex structure
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / Preq1 / Glycosyltransferase / Metal-binding / Queuosine biosynthesis / tRNA processing
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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
DepositionDec 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,2965
Polymers42,8681
Non-polymers4294
Water4,504250
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,59310
Polymers85,7352
Non-polymers8588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5000 Å2
ΔGint-15 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.655, 64.878, 70.328
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1250-

HOH

21A-1326-

HOH

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Components

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


Mass: 42867.625 Da / Num. of mol.: 1 / Mutation: Y106F,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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.27 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97803 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97803 Å / Relative weight: 1
ReflectionResolution: 1.19→8 Å / Num. all: 224997 / Num. obs: 116963 / % possible obs: 91 % / Redundancy: 3.7 % / Rsym value: 0.041 / Net I/σ(I): 21

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bl3

3bl3


Resolution: 1.19→8 Å / Num. parameters: 26800 / Num. restraintsaints: 33645 / 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 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 -5 %RANDOM
Rwork0.1508 ---
all0.1512 116963 --
obs-116963 91 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 2579 / Occupancy sum non hydrogen: 2925
Refinement stepCycle: LAST / Resolution: 1.19→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 26 250 2930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0252
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.074

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