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- PDB-4puj: tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2... -

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Basic information

Entry
Database: PDB / ID: 4puj
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2-(morpholin-4-yl)ethyl]amino}-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-CKR / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
SupersessionJul 16, 2014ID: 3C2N
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 / 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)43,7248
Polymers42,9261
Non-polymers7997
Water6,990388
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,44916
Polymers85,8512
Non-polymers1,59714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6760 Å2
ΔGint-39 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.582, 64.843, 71.016
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21A-820-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42925.703 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme
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

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Non-polymers , 5 types, 395 molecules

#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CKR / 6-amino-2-[(2-morpholin-4-ylethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 6-Amino-2-[(2-morpholin-4-ylethyl)amino]-8-oxo-7,8-dihydro-1H-imidazo[4,5-G]quinazolin


Mass: 329.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N7O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 49.07 %
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: 1.42→30 Å / Num. obs: 76897 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 28.6
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3785 / Rsym value: 0.505 / % possible all: 98.4

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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: 1.42→27.24 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 2000 2.6 %Random
Rwork0.129 ---
obs0.1298 76891 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 50 388 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053036
X-RAY DIFFRACTIONf_angle_d1.0374108
X-RAY DIFFRACTIONf_dihedral_angle_d12.4471166
X-RAY DIFFRACTIONf_chiral_restr0.066430
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4174-1.45280.21271380.16095181X-RAY DIFFRACTION97
1.4528-1.49210.19211430.1335316X-RAY DIFFRACTION98
1.4921-1.5360.18041400.11685266X-RAY DIFFRACTION99
1.536-1.58560.14891430.10575334X-RAY DIFFRACTION99
1.5856-1.64220.13361420.09825327X-RAY DIFFRACTION99
1.6422-1.7080.14041420.10245318X-RAY DIFFRACTION99
1.708-1.78570.16321420.10345356X-RAY DIFFRACTION100
1.7857-1.87980.15461440.10745361X-RAY DIFFRACTION100
1.8798-1.99750.15311430.11535364X-RAY DIFFRACTION100
1.9975-2.15170.14831440.11665394X-RAY DIFFRACTION100
2.1517-2.36810.15861440.12265366X-RAY DIFFRACTION100
2.3681-2.71060.15031440.14215407X-RAY DIFFRACTION100
2.7106-3.4140.15461450.13945444X-RAY DIFFRACTION100
3.414-27.2450.17451460.14715457X-RAY DIFFRACTION99

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