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- PDB-5jt7: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5jt7
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 1-(2-((2-morpholinoethyl)amino)-1H-benzo[d]imidazol-6-yl)guanidine
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-6N2 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4795
Polymers42,9261
Non-polymers5534
Water3,729207
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,95710
Polymers85,8512
Non-polymers1,1068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area4250 Å2
ΔGint-19 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.322, 64.214, 71.238
Angle α, β, γ (deg.)90.00, 93.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21A-702-

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 (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli)
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-6N2 / N-(2-{[2-(morpholin-4-yl)ethyl]amino}-1H-benzimidazol-5-yl)guanidine


Mass: 303.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N7O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 48.7 %
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: Aug 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.7→42.8 Å / Num. obs: 44054 / % possible obs: 98.1 % / Redundancy: 2.5 % / Rsym value: 0.031 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.02 / % possible all: 98.4

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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: 1.7→42.8 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2203 5 %random selection
Rwork0.1715 ---
obs0.1731 44050 98.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 28 207 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062953
X-RAY DIFFRACTIONf_angle_d0.8373990
X-RAY DIFFRACTIONf_dihedral_angle_d16.9121785
X-RAY DIFFRACTIONf_chiral_restr0.051416
X-RAY DIFFRACTIONf_plane_restr0.006551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73620.38411390.31942640X-RAY DIFFRACTION98
1.7362-1.77650.28491360.27142585X-RAY DIFFRACTION98
1.7765-1.8210.27851350.24032569X-RAY DIFFRACTION99
1.821-1.87020.2961390.23032630X-RAY DIFFRACTION98
1.8702-1.92520.27041370.21592606X-RAY DIFFRACTION98
1.9252-1.98740.26521370.18962616X-RAY DIFFRACTION98
1.9874-2.05840.23611380.18712623X-RAY DIFFRACTION99
2.0584-2.14080.21051380.17522606X-RAY DIFFRACTION98
2.1408-2.23820.1881370.16652600X-RAY DIFFRACTION98
2.2382-2.35620.19191390.16282640X-RAY DIFFRACTION99
2.3562-2.50390.20581380.16182630X-RAY DIFFRACTION99
2.5039-2.69720.18921380.1692621X-RAY DIFFRACTION98
2.6972-2.96850.19731390.17112639X-RAY DIFFRACTION99
2.9685-3.39790.1971390.16192647X-RAY DIFFRACTION98
3.3979-4.28040.16481360.1562588X-RAY DIFFRACTION96
4.2804-42.80.20761380.15982607X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7644-0.23760.44160.526-0.16621.1598-0.0889-0.18880.09390.17360.0866-0.0606-0.0457-0.0138-0.00930.2890.0446-0.00070.2295-0.02730.229199.07573.805918.1914
21.0276-0.3791-1.16081.3222-0.37481.8903-0.09090.00710.54670.10870.15-0.3244-0.7055-0.0385-0.14630.7720.0799-0.0620.4162-0.11790.539597.896625.232127.081
31.6913-0.31190.32220.97850.80551.7279-0.1151-0.38760.45540.15540.0853-0.0978-0.35820.029-0.00410.50470.0985-0.00720.4398-0.07810.322696.955612.828829.4233
41.8664-0.0456-0.77541.45260.39072.15490.0382-0.43050.35930.27420.1212-0.1673-0.24260.2508-0.16020.35220.0222-0.0390.331-0.09520.3473111.646512.540625.0396
50.808-0.18870.76270.7868-0.31011.2083-0.06420.20840.0415-0.08680.0121-0.15530.06030.240.06340.184-0.00960.02630.22260.00160.2241108.1356.3988-2.6021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:105)
2X-RAY DIFFRACTION2(chain A and resid 106:135)
3X-RAY DIFFRACTION3(chain A and resid 136:159)
4X-RAY DIFFRACTION4(chain A and resid 160:289)
5X-RAY DIFFRACTION5(chain A and resid 290:382)

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