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- PDB-3hfy: Mutant of tRNA-guanine transglycosylase (K52M) -

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Basic information

Entry
Database: PDB / ID: 3hfy
TitleMutant of tRNA-guanine transglycosylase (K52M)
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / dimer interface / mutation / Glycosyltransferase / Metal-binding / Queuosine biosynthesis / tRNA processing / Zinc
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsRitschel, T. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: An Integrative Approach Combining Noncovalent Mass Spectrometry, Enzyme Kinetics and X-ray Crystallography to Decipher Tgt Protein-Protein and Protein-RNA Interaction
Authors: Ritschel, T. / Atmanene, C. / Reuter, K. / Van Dorsselaer, A. / Sanglier-Cianferani, S. / Klebe, G.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)42,9932
Polymers42,9281
Non-polymers651
Water1,78399
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9864
Polymers85,8552
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.600, 65.200, 71.600
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42927.723 Da / Num. of mol.: 1 / Mutation: K52M
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Sequence details312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J. ...312TH RESIDUE IS LYS ACCORDING TO REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)] AND AHN J.Y. ET AL [SUBMITTED (OCT-2000) TO THE EMBL/GENBANK/DDBJ DATABASES]

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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: 2.3 Å3/Da / Density % sol: 46.45 %
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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 4, 2009 / Details: Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 26320 / Num. obs: 26320 / % possible obs: 99.2 % / Redundancy: 4.2 % / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Mean I/σ(I) obs: 7.7 / Num. unique all: 1301 / % possible all: 99

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→10 Å / Num. parameters: 10903 / Num. restraintsaints: 10803 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 1210 4.8 %RANDOM
all0.204 25041 --
obs0.2165 25041 96 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2722
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 1 99 2716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0198
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.074
X-RAY DIFFRACTIONs_approx_iso_adps0

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