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- PDB-5jt5: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5jt5
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-((2-morpholinoethyl)amino)-1H-benzo[d]imidazole-5-carboxamide
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Benzimidazole-derivatives / shigellosis / TRANSFERASE INHIBITOR
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-6NK / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines.
Authors: Ehrmann, F.R. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,6548
Polymers42,9261
Non-polymers7297
Water7,584421
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30816
Polymers85,8512
Non-polymers1,45714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5650 Å2
ΔGint-35 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.293, 65.276, 70.641
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-557-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 428 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.: 3 / 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-6NK / 2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazole-6-carboxamide


Mass: 289.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N5O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.21→43.53 Å / Num. obs: 122593 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rsym value: 0.041 / Net I/σ(I): 15.68
Reflection shellResolution: 1.21→1.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.28 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.21→39.8 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.38
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 6129 5 %random selection
Rwork0.135 ---
obs0.136 122586 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.21→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 39 421 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053112
X-RAY DIFFRACTIONf_angle_d0.8054210
X-RAY DIFFRACTIONf_dihedral_angle_d22.4991191
X-RAY DIFFRACTIONf_chiral_restr0.072439
X-RAY DIFFRACTIONf_plane_restr0.005578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.22330.22531950.21343710X-RAY DIFFRACTION96
1.2233-1.23770.24512020.20373827X-RAY DIFFRACTION97
1.2377-1.25280.20891960.19253723X-RAY DIFFRACTION96
1.2528-1.26860.2212020.18353841X-RAY DIFFRACTION97
1.2686-1.28530.18711990.17053779X-RAY DIFFRACTION98
1.2853-1.30290.20652030.1653868X-RAY DIFFRACTION98
1.3029-1.32160.18332010.15643816X-RAY DIFFRACTION99
1.3216-1.34130.18132040.15813874X-RAY DIFFRACTION98
1.3413-1.36230.17732030.15223862X-RAY DIFFRACTION98
1.3623-1.38460.1592030.14483854X-RAY DIFFRACTION98
1.3846-1.40850.17712030.13753859X-RAY DIFFRACTION99
1.4085-1.43410.14982070.12763920X-RAY DIFFRACTION99
1.4341-1.46170.14712030.12213871X-RAY DIFFRACTION99
1.4617-1.49150.14882030.11333842X-RAY DIFFRACTION99
1.4915-1.52390.15272040.11283875X-RAY DIFFRACTION99
1.5239-1.55940.14432060.113921X-RAY DIFFRACTION99
1.5594-1.59840.152060.11043922X-RAY DIFFRACTION99
1.5984-1.64160.13582070.11043929X-RAY DIFFRACTION100
1.6416-1.68990.15662050.11833898X-RAY DIFFRACTION100
1.6899-1.74440.1492050.12673897X-RAY DIFFRACTION100
1.7444-1.80680.15372080.12433937X-RAY DIFFRACTION100
1.8068-1.87910.16722050.12283906X-RAY DIFFRACTION100
1.8791-1.96470.1552070.12813928X-RAY DIFFRACTION100
1.9647-2.06820.14552070.12983927X-RAY DIFFRACTION100
2.0682-2.19780.14872060.13083919X-RAY DIFFRACTION100
2.1978-2.36750.1522050.13243898X-RAY DIFFRACTION99
2.3675-2.60570.16562080.13963959X-RAY DIFFRACTION99
2.6057-2.98260.15012080.1423939X-RAY DIFFRACTION100
2.9826-3.75730.14092080.13213949X-RAY DIFFRACTION99
3.7573-39.80.15822100.14134007X-RAY DIFFRACTION99

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