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- PDB-5lpt: tRNA guanine Transglycosylase (TGT) in co-crystallized complex (s... -

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Basic information

Entry
Database: PDB / ID: 5lpt
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex (space group P21) with 6-amino-2-(methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5,6-tetramethoxytetrahydro-2H-pyran-2-yl)ethyl)-1H-imidazo[4,5-g]quinazolin-8(7H)-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Carbohydrate-based Inhibitors / homodimer / 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
Chem-726 / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Carbohydrate-based Inhibitors targeting the Ribose-34 pocket of Z.mobilis TGT and changing the oligomeric state of the homodimer
Authors: Ehrmann, F.R. / Botzanowski, T. / Pfaffender, T. / Heine, A. / Diederich, F. / Sanglier-Cianferani, S. / Klebe, G.
History
DepositionAug 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 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
B: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1849
Polymers85,8512
Non-polymers1,3327
Water3,549197
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-16 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.745, 78.866, 84.891
Angle α, β, γ (deg.)90.00, 108.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42925.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
Gene: tgt, ZMO0363 / Variant: ATCC 31821 / ZM4 / CP4 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-726 / 6-azanyl-2-(methylamino)-4-[2-[(2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5,6-tetramethoxyoxan-2-yl]ethyl]-1,7-dihydroimidazo[4,5-g]quinazolin-8-one


Mass: 462.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
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 PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.36→48.29 Å / Num. obs: 35384 / % possible obs: 99 % / Redundancy: 3.4 % / Rsym value: 0.118 / Net I/σ(I): 8.1
Reflection shellResolution: 2.36→2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.6 / % possible all: 96.6

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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: 2.36→40.51 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.57
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1769 5 %5% random selection
Rwork0.201 ---
obs0.2026 35371 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.36→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 86 197 5769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065701
X-RAY DIFFRACTIONf_angle_d0.7027689
X-RAY DIFFRACTIONf_dihedral_angle_d16.3083407
X-RAY DIFFRACTIONf_chiral_restr0.044815
X-RAY DIFFRACTIONf_plane_restr0.0051059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.41960.30831270.25172405X-RAY DIFFRACTION93
2.4196-2.49080.2831370.24742605X-RAY DIFFRACTION100
2.4908-2.57120.28211360.23372573X-RAY DIFFRACTION100
2.5712-2.66310.25721350.22792583X-RAY DIFFRACTION100
2.6631-2.76970.26751360.21962573X-RAY DIFFRACTION100
2.7697-2.89570.25931370.22192614X-RAY DIFFRACTION100
2.8957-3.04830.23871360.22452576X-RAY DIFFRACTION100
3.0483-3.23930.26071370.20642605X-RAY DIFFRACTION100
3.2393-3.48920.23691360.20632588X-RAY DIFFRACTION100
3.4892-3.84010.21171370.18042599X-RAY DIFFRACTION100
3.8401-4.39520.20091380.16662612X-RAY DIFFRACTION100
4.3952-5.53530.18851370.17252615X-RAY DIFFRACTION100
5.5353-40.510.22741400.20052654X-RAY DIFFRACTION99
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)
10.1696-0.2606-0.0170.69780.48340.63610.13470.0003-0.0309-0.0290.0413-0.27950.05030.0489-0.00010.165-0.0022-0.00810.20590.00080.26874.1923-10.45178.7063
20.6731-0.3489-0.63730.96620.16521.40480.2622-0.0149-0.26850.4272-0.3323-0.28910.1181-0.29620.04920.2569-0.0272-0.06840.23010.00050.4155-6.9273-32.164880.8685
30.07720.1190.13690.2050.25530.3337-0.002-0.2647-0.20590.12480.0409-0.2650.09970.17990.00070.154-0.0017-0.02940.1846-0.03190.35233.571-23.105482.7122
40.51870.39840.18761.6766-0.0230.9910.0415-0.3128-0.10150.35230.0655-0.02430.1098-0.03510.02420.2277-0.0199-0.07270.24630.02350.2119-2.6872-14.903392.7431
50.26020.01930.37330.6494-0.04770.77440.00550.07920.0719-0.07480.0268-0.0334-0.0822-0.034200.15560.02220.01870.2181-0.01470.2196-14.39844.572875.4578
60.70920.48250.39391.0445-0.42340.8724-0.01280.1454-0.114-0.14440.0702-0.2276-0.01160.15650.00010.3151-0.00020.05520.2629-0.02470.2388-13.9418-15.596243.7231
70.13010.1694-0.08970.2488-0.04050.22670.18870.02350.0995-0.1531-0.12510.18060.08340.1359-0.00010.46470.08110.02490.2946-0.02710.2813-22.41886.429951.6029
80.0855-0.02220.04890.1378-0.04260.22-0.2140.28520.065-0.13350.08530.0185-0.3201-0.0536-0.00020.4205-0.02250.02440.247-0.02060.2427-17.5166-2.323941.7889
90.5850.2584-0.07871.41790.42570.3695-0.0780.17150.0695-0.1883-0.00060.2363-0.1981-0.2442-0.03030.38930.0349-0.04940.2724-0.00730.1831-29.6308-10.658541.2046
100.1768-0.00020.23210.5452-0.28990.59040.062-0.12-0.1818-0.04580.0485-0.01190.2487-0.15530.00010.2286-0.01880.01790.23170.00380.2242-21.9214-30.271360.7684
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)
6X-RAY DIFFRACTION6(chain B and resid 11:105)
7X-RAY DIFFRACTION7(chain B and resid 106:135)
8X-RAY DIFFRACTION8(chain B and resid 136:159)
9X-RAY DIFFRACTION9(chain B and resid 160:289)
10X-RAY DIFFRACTION10(chain B and resid 290:382)

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