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- PDB-5i03: tRNA-guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5i03
TitletRNA-guanine Transglycosylase (TGT) in co-crystallized complex with 6-Amino-4-[2-(4-methylphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / co-crystallization / 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-NEZ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Co-crystallization, Isothermal titration calorimetry and nanoESI-MS reveal dimer disturbing inhibitors
Authors: Ehrmann, F.R. / Stojko, J. / Heine, A. / Diederich, F. / Reuter, K. / Sanglier-Cianferani, S. / Klebe, G.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 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)43,5576
Polymers42,9261
Non-polymers6315
Water3,963220
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,11312
Polymers85,8512
Non-polymers1,26210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area5480 Å2
ΔGint-23 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.140, 64.641, 71.017
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number5
Space group name H-MC121

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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 , 5 types, 225 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NEZ / 6-AMINO-4-[2-(4-METHYLPHENYL)ETHYL]-1,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE


Mass: 319.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.73→42.49 Å / Num. obs: 38683 / % possible obs: 95.7 % / Redundancy: 2.9 % / Rsym value: 0.056 / Net I/σ(I): 14.5
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.2 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1492refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.73→42.486 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1935 5 %random selection
Rwork0.181 ---
obs0.1821 38682 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→42.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 41 220 2975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062903
X-RAY DIFFRACTIONf_angle_d0.833922
X-RAY DIFFRACTIONf_dihedral_angle_d18.4771749
X-RAY DIFFRACTIONf_chiral_restr0.051413
X-RAY DIFFRACTIONf_plane_restr0.006548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7279-1.77110.30771350.26722562X-RAY DIFFRACTION94
1.7711-1.8190.26451370.25432602X-RAY DIFFRACTION96
1.819-1.87260.2571390.23572644X-RAY DIFFRACTION97
1.8726-1.9330.26041410.23532680X-RAY DIFFRACTION98
1.933-2.00210.24011390.21412640X-RAY DIFFRACTION97
2.0021-2.08220.22261410.19612668X-RAY DIFFRACTION97
2.0822-2.1770.23141390.18782642X-RAY DIFFRACTION97
2.177-2.29180.21691380.18572631X-RAY DIFFRACTION96
2.2918-2.43540.22451400.1812648X-RAY DIFFRACTION97
2.4354-2.62340.19021390.18092642X-RAY DIFFRACTION97
2.6234-2.88730.19181360.16822591X-RAY DIFFRACTION95
2.8873-3.3050.18051400.15492652X-RAY DIFFRACTION96
3.305-4.16340.15271360.1482584X-RAY DIFFRACTION94
4.1634-42.49870.19651350.17982561X-RAY DIFFRACTION91
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)
14.6469-1.8861-0.02771.12840.11121.19340.08970.1972-0.1605-0.0802-0.07470.0933-0.0041-0.1109-0.02210.1973-0.0071-0.02570.1549-0.00430.151694.13083.088419.3556
22.3094-2.7709-0.93873.45951.85366.59570.22880.18580.2996-0.7985-0.2371-0.2568-1.2752-0.69440.05380.53250.0792-0.0440.2534-0.01340.305993.649725.703128.0235
35.95432.51320.86924.5932.2323.2187-0.0397-0.14410.35240.00190.04720.2227-0.0108-0.1543-0.00580.13750.0321-0.02540.14280.02790.125192.623613.361129.3502
41.3608-0.0409-0.3691.31390.15061.54340.0262-0.03610.0744-0.05520.0333-0.0921-0.16590.0684-0.06090.15420.0102-0.01250.1292-0.0020.1301106.722212.652425.3068
52.7663-1.66023.23041.7107-2.61214.80890.02210.10630.0692-0.1066-0.0181-0.00350.07930.1176-0.01130.1727-0.00080.01220.1299-0.02350.1384102.35156.2182-2.1678
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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