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- PDB-4puk: tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-(me... -

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Basic information

Entry
Database: PDB / ID: 4puk
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
Keywordstransferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / Guanine / preQ1 / tRNA / transferase-transferase inhibitor complex
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-2WU / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme.
Authors: Neeb, M. / Czodrowski, P. / Heine, A. / Barandun, L.J. / Hohn, C. / Diederich, F. / Klebe, G.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,4986
Polymers42,9261
Non-polymers5725
Water6,575365
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,99512
Polymers85,8512
Non-polymers1,14410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4980 Å2
ΔGint-16 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.788, 64.986, 70.987
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-841-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM4 / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2WU / 6-amino-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 230.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. ...AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995))

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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: 49.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 / 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: 1.49→30 Å / Num. obs: 66573 / % possible obs: 99.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 29.3
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3339 / Rsym value: 0.481 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.49→27.299 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.33 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 2000 3.01 %Random
Rwork0.1385 ---
obs0.1396 66504 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→27.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 36 365 3250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133035
X-RAY DIFFRACTIONf_angle_d1.3664112
X-RAY DIFFRACTIONf_dihedral_angle_d12.4491164
X-RAY DIFFRACTIONf_chiral_restr0.089435
X-RAY DIFFRACTIONf_plane_restr0.008566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4902-1.52750.20591390.13464501X-RAY DIFFRACTION98
1.5275-1.56880.18221420.1274577X-RAY DIFFRACTION99
1.5688-1.6150.1751420.11524576X-RAY DIFFRACTION99
1.615-1.66710.16171420.11194578X-RAY DIFFRACTION99
1.6671-1.72670.15091430.10944608X-RAY DIFFRACTION99
1.7267-1.79580.15511430.10794593X-RAY DIFFRACTION99
1.7958-1.87750.17241410.11954572X-RAY DIFFRACTION99
1.8775-1.97640.21991440.15544631X-RAY DIFFRACTION99
1.9764-2.10020.16731430.12024616X-RAY DIFFRACTION100
2.1002-2.26230.1691430.13274622X-RAY DIFFRACTION100
2.2623-2.48990.17431430.13914614X-RAY DIFFRACTION99
2.4899-2.84980.15381450.14514657X-RAY DIFFRACTION100
2.8498-3.58920.16641440.14734669X-RAY DIFFRACTION100
3.5892-27.30360.17951460.15234690X-RAY DIFFRACTION99

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