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- PDB-5j9m: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5j9m
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-(methylamino)-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-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
2-(methylamino)-1H-benzimidazole-5-carboxamide / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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
DepositionApr 10, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)43,4637
Polymers42,9261
Non-polymers5376
Water7,152397
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92614
Polymers85,8512
Non-polymers1,07512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5010 Å2
ΔGint-38 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.971, 64.946, 70.662
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-868-

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)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 403 molecules

#2: Chemical ChemComp-6HD / 2-(methylamino)-1H-benzimidazole-5-carboxamide


Mass: 190.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N4O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.4 Å3/Da / Density % sol: 49.01 %
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: 14.3 / Wavelength: 0.895 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.33→45.21 Å / Num. obs: 93288 / % possible obs: 99.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.045 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shellResolution: 1.33→1.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1492: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.33→45.21 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1571 4662 5 %
Rwork0.1294 --
obs0.1308 93249 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 32 397 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053114
X-RAY DIFFRACTIONf_angle_d0.8084219
X-RAY DIFFRACTIONf_dihedral_angle_d21.3521176
X-RAY DIFFRACTIONf_chiral_restr0.071439
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.3440.27961450.24432754X-RAY DIFFRACTION93
1.344-1.35980.26711570.22212980X-RAY DIFFRACTION100
1.3598-1.37640.231530.20872917X-RAY DIFFRACTION100
1.3764-1.39380.23241570.19622969X-RAY DIFFRACTION100
1.3938-1.41220.23251570.1892977X-RAY DIFFRACTION100
1.4122-1.43150.20971560.18742969X-RAY DIFFRACTION100
1.4315-1.4520.2331520.17142893X-RAY DIFFRACTION100
1.452-1.47360.1941580.16253001X-RAY DIFFRACTION100
1.4736-1.49670.18161550.14292947X-RAY DIFFRACTION100
1.4967-1.52120.19031550.13572938X-RAY DIFFRACTION100
1.5212-1.54740.16721570.13022983X-RAY DIFFRACTION100
1.5474-1.57560.14151550.12362950X-RAY DIFFRACTION100
1.5756-1.60590.15451560.11242970X-RAY DIFFRACTION100
1.6059-1.63870.14221550.11152941X-RAY DIFFRACTION100
1.6387-1.67430.13631560.1082966X-RAY DIFFRACTION100
1.6743-1.71330.15071570.11352987X-RAY DIFFRACTION100
1.7133-1.75610.14811580.10762987X-RAY DIFFRACTION100
1.7561-1.80360.14311560.10822966X-RAY DIFFRACTION100
1.8036-1.85670.14661550.10732945X-RAY DIFFRACTION100
1.8567-1.91660.13231570.11272981X-RAY DIFFRACTION100
1.9166-1.98510.13921540.11652930X-RAY DIFFRACTION99
1.9851-2.06460.15151560.11472975X-RAY DIFFRACTION99
2.0646-2.15850.13451560.11242960X-RAY DIFFRACTION99
2.1585-2.27230.14851550.1212946X-RAY DIFFRACTION99
2.2723-2.41470.17251570.12352986X-RAY DIFFRACTION99
2.4147-2.60110.15021550.13322942X-RAY DIFFRACTION99
2.6011-2.86280.1531560.13072968X-RAY DIFFRACTION99
2.8628-3.2770.15741570.1312973X-RAY DIFFRACTION99
3.277-4.12820.13111560.11732970X-RAY DIFFRACTION99
4.1282-45.23660.15941530.14042916X-RAY DIFFRACTION95

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