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- PDB-5egr: tRNA guanine transglycosylase (TGT) in complex with an Immucillin... -

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Basic information

Entry
Database: PDB / ID: 5egr
TitletRNA guanine transglycosylase (TGT) in complex with an Immucillin derivative
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Transition state analog / shigellosis / Immucillin / modeling / TRANSFERASE INHIBITOR
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine 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-5NT / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Synthesis of an Immucillin Derivative as a Class of tRNA-Guanine Transglycosylase Inhibitors: Exploration of a Transition State Analogous Binding Mode
Authors: Ehrmann, F.R. / Hohn, C. / Haertsch, A. / Trapp, N. / Heine, A. / Klebe, G. / Diederich, F.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jan 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)43,6878
Polymers42,9261
Non-polymers7617
Water3,927218
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,37416
Polymers85,8512
Non-polymers1,52214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area5170 Å2
ΔGint-18 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.458, 64.485, 70.978
Angle α, β, γ (deg.)90.00, 93.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

21A-714-

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 , 5 types, 225 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / 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-5NT / 2-azanyl-7-[(2~{S},3~{R},5~{S})-5-(hydroxymethyl)-3-oxidanyl-pyrrolidin-2-yl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one


Mass: 265.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.81 %
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: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.55→42.854 Å / Num. obs: 58639 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.849 % / Rsym value: 0.032 / Net I/σ(I): 15.53
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 2.8306 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(dev-2006_1492: ???)refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.55→42.854 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 2932 5 %random selection
Rwork0.1722 ---
obs0.1731 58635 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→42.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 48 218 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072960
X-RAY DIFFRACTIONf_angle_d1.0493996
X-RAY DIFFRACTIONf_dihedral_angle_d12.6351107
X-RAY DIFFRACTIONf_chiral_restr0.05422
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57460.29311350.28332582X-RAY DIFFRACTION97
1.5746-1.60170.24111380.26572621X-RAY DIFFRACTION99
1.6017-1.63090.27531410.2532665X-RAY DIFFRACTION100
1.6309-1.66220.28371390.23332638X-RAY DIFFRACTION99
1.6622-1.69620.27131390.22612657X-RAY DIFFRACTION99
1.6962-1.73310.2341400.2172648X-RAY DIFFRACTION99
1.7331-1.77340.22091400.19512669X-RAY DIFFRACTION100
1.7734-1.81770.2211400.19432648X-RAY DIFFRACTION100
1.8177-1.86690.22731390.18762643X-RAY DIFFRACTION100
1.8669-1.92180.24891420.18632692X-RAY DIFFRACTION99
1.9218-1.98380.19761380.1762633X-RAY DIFFRACTION99
1.9838-2.05470.20421400.17052661X-RAY DIFFRACTION99
2.0547-2.1370.19821400.16632656X-RAY DIFFRACTION99
2.137-2.23430.17641390.17182632X-RAY DIFFRACTION99
2.2343-2.3520.20741400.16592661X-RAY DIFFRACTION99
2.352-2.49940.19731400.16852672X-RAY DIFFRACTION99
2.4994-2.69230.15751400.17132660X-RAY DIFFRACTION99
2.6923-2.96320.19541410.16592677X-RAY DIFFRACTION99
2.9632-3.39190.19641400.1652660X-RAY DIFFRACTION99
3.3919-4.27280.16251400.15362657X-RAY DIFFRACTION98
4.2728-42.87020.16941410.16632671X-RAY DIFFRACTION97
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)
12.4107-0.48140.30520.95920.00971.1661-0.1722-0.32410.0480.30780.146-0.0321-0.0666-0.09390.00790.2440.0584-0.00640.1838-0.01530.142999.1933.971618.0751
26.4602-6.2379-3.33658.49074.23144.53950.0953-0.09330.9374-0.2578-0.2941-0.6631-1.236-0.45160.19880.62570.1296-0.06170.4361-0.13060.620599.32325.973229.0895
36.09840.27830.45235.87944.98718.15980.032-0.56180.5970.3575-0.0255-0.0214-0.303-0.1428-0.09970.42760.1135-0.00310.3666-0.05220.208497.648513.633429.2687
42.2205-0.1175-0.71821.79520.38212.6668-0.0004-0.53230.40390.41110.1453-0.2757-0.19180.1664-0.12640.34190.0394-0.0840.3076-0.09970.3385111.777313.141425.299
51.8387-0.71971.62141.3218-0.97352.3551-0.09140.21710.1091-0.0646-0.0008-0.22770.01340.29440.10820.1711-0.02120.02730.2143-0.01250.2206108.31067.2328-2.4937
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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