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- PDB-2pwv: tRNA guanine transglycosylase E235Q mutant in complex with preQ0 -

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Basic information

Entry
Database: PDB / ID: 2pwv
TitletRNA guanine transglycosylase E235Q mutant in complex with preQ0
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / E235Q mutant / preQ0
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
Chem-PQ0 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.7 Å
AuthorsTidten, N. / Stengl, B. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies.
Authors: Tidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K.
History
DepositionMay 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999sequence THERE IS A THR -> LYS SEQUENCE CONFLICT AT RESIDUE 312 IN THE UNIPROT DATABASE.

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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)43,7189
Polymers42,9251
Non-polymers7938
Water4,107228
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,43618
Polymers85,8492
Non-polymers1,58616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.757, 65.175, 70.455
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-865-

HOH

21A-884-

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: 42924.719 Da / Num. of mol.: 1 / Mutation: E235Q
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) 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-PQ0 / 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE / 7-DEAZA-7-CYANO-GUANINE


Mass: 175.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5N5O
#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.: 228 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 40368 / % possible obs: 0.983 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.491 / % possible all: 0.969

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-3000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: pdb entry 1P0B

1p0b


Resolution: 1.7→10 Å / Num. parameters: 12665 / Num. restraintsaints: 12244 / 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
Rfree0.2451 --RANDOM
Rwork0.2006 ---
obs0.2006 40368 90 %-
Solvent computationSolvent model: BABINET (SWAT)
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 2812 / Occupancy sum non hydrogen: 3151
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 50 228 3076
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0

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