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- PDB-3tll: tRNA-Guanine Transglycosylase in complex with N-Ethyl-lin-benzogu... -

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Basic information

Entry
Database: PDB / ID: 3tll
TitletRNA-Guanine Transglycosylase in complex with N-Ethyl-lin-benzoguanine Inhibitor
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TIM BARREL / GLYCOSYLTRANSFERASE / METAL-BINDING / QUEUOSINE / BIOSYNTHESIS / TRANSFERASE / TRNA PROCESSING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
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-62D / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.37 Å
AuthorsKlebe, G. / Immekus, F. / Heine, A.
CitationJournal: Chemistry / Year: 2012
Title: From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters.
Authors: Barandun, L.J. / Immekus, F. / Kohler, P.C. / Tonazzi, S. / Wagner, B. / Wendelspiess, S. / Ritschel, T. / Heine, A. / Kansy, M. / Klebe, G. / Diederich, F.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5266
Polymers42,9261
Non-polymers6005
Water6,630368
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,05112
Polymers85,8512
Non-polymers1,20010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4390 Å2
ΔGint-17 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.193, 64.836, 70.329
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1171-

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 (bacteria) / Gene: tgt, ZMO0363 / 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: 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-62D / 6-(ethylamino)-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 258.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.23 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100MM TRIS HCL, 1MM DTT, 10% DMSO, 5% PEG8000, 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 MX-225 / Detector: CCD / Date: Dec 10, 2010 / Details: Rh-coated silicon with indirect water cooling
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. all: 81623 / Num. obs: 81623 / % possible obs: 95 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.52 Å2 / Rsym value: 0.031 / Net I/σ(I): 25.24
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 3991 / Rsym value: 0.131 / % possible all: 94.5

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO
Starting model: 1POD

1pod


Resolution: 1.37→30 Å / Num. parameters: 29558 / Num. restraintsaints: 37055 / Cross valid method: FREE R / σ(F): 0 / σ(I): 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. THE TEST SET WAS USED THROUGHOUT STRUCTURE REFINEMENT, ONLY IN THE LAST REFINEMENT CYCLE ALL ...Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56. THE TEST SET WAS USED THROUGHOUT STRUCTURE REFINEMENT, ONLY IN THE LAST REFINEMENT CYCLE ALL REFLECTIONS WERE USED FOR R FACTOR CALCULATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1677 4027 -RANDOM
Rwork0.126 ---
all0.127 80045 --
obs0.127 76018 93.5 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3189.47
Refinement stepCycle: LAST / Resolution: 1.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 38 368 3186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0251
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.078

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