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- PDB-2z1w: tRNA guanine transglycosylase TGT E235Q mutant in complex with BD... -

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Basic information

Entry
Database: PDB / ID: 2z1w
TitletRNA guanine transglycosylase TGT E235Q mutant in complex with BDI (2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE)
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / E235Q mutant / BDI / BIH / 2-BUTYL-5 / 6-DIHYDRO-1H-IMIDAZO[4 / 5-D]PYRIDAZINE-4 / 7-DIONE
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
Chem-BDI / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsTidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K.
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 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE CONFLICT INVOLVING RESIDUE 312 IS CONSISTENT WITH THE REF. 1 AND 2 IN THE UNIPROT ...SEQUENCE THE CONFLICT INVOLVING RESIDUE 312 IS CONSISTENT WITH THE 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)44,02712
Polymers42,9251
Non-polymers1,10211
Water5,368298
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,05424
Polymers85,8492
Non-polymers2,20522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8790 Å2
ΔGint-11 kcal/mol
Surface area24600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.878, 65.324, 70.615
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-866-

HOH

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Components

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


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-BDI / 2-BUTYL-5,6-DIHYDRO-1H-IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE


Mass: 208.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 8% PEG 8000, 100mM MES pH 5.5, 1mM DTT, 10% DMSO, pH 5.50, 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 47068 / % possible obs: 92.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 33

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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 1P0B

1p0b


Resolution: 1.63→26.46 Å / Num. parameters: 29385 / Num. restraintsaints: 37071 / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 -5 %RANDOM
all0.1339 ---
obs0.1318 44520 92.5 %-
Solvent computationSolvent model: BABINET (SWAT)
Refine analyzeNum. disordered residues: 16 / Occupancy sum hydrogen: 2744 / Occupancy sum non hydrogen: 3172.5
Refinement stepCycle: LAST / Resolution: 1.63→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 70 298 3168
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_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.071

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