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- PDB-5v3c: Crystal structure of TGT in complex with 4-(aminomethane)cyclohex... -

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Basic information

Entry
Database: PDB / ID: 5v3c
TitleCrystal structure of TGT in complex with 4-(aminomethane)cyclohexane-1-carboxylic acid
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / TRNA / Guanine exchange enzyme / transglycosylase
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
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.419 Å
AuthorsHassaan, E. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2020
Title: Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies.
Authors: Hassaan, E. / Eriksson, P.O. / Geschwindner, S. / Heine, A. / Klebe, G.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / 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.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Mar 18, 2020Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Jan 17, 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)42,5058
Polymers41,7631
Non-polymers7417
Water3,981221
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,01016
Polymers83,5272
Non-polymers1,48314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area6070 Å2
ΔGint18 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.746, 63.739, 70.430
Angle α, β, γ (deg.)90.00, 92.59, 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: 41763.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt, ZMO0363 / Plasmid: PPR-IBA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase

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Non-polymers , 6 types, 228 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO2 / Comment: medication*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting 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 PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.419→44.328 Å / Num. obs: 73715 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rsym value: 0.046 / Net I/σ(I): 15.59
Reflection shellResolution: 1.42→1.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.06 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LBU

4lbu


Resolution: 1.419→44.328 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1554 3686 5 %
Rwork0.1335 --
obs0.1346 73705 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.419→44.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 44 221 3120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072991
X-RAY DIFFRACTIONf_angle_d0.9444027
X-RAY DIFFRACTIONf_dihedral_angle_d22.9421112
X-RAY DIFFRACTIONf_chiral_restr0.072424
X-RAY DIFFRACTIONf_plane_restr0.006534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4192-1.43790.3241400.28962651X-RAY DIFFRACTION96
1.4379-1.45760.24351370.24952608X-RAY DIFFRACTION99
1.4576-1.47840.2371410.20672686X-RAY DIFFRACTION99
1.4784-1.50050.20091390.17842643X-RAY DIFFRACTION99
1.5005-1.52390.21491410.16452679X-RAY DIFFRACTION99
1.5239-1.54890.24781410.15752676X-RAY DIFFRACTION99
1.5489-1.57560.18251410.14592670X-RAY DIFFRACTION99
1.5756-1.60430.16951410.13592690X-RAY DIFFRACTION99
1.6043-1.63510.17841420.13362683X-RAY DIFFRACTION100
1.6351-1.66850.17241410.1332688X-RAY DIFFRACTION100
1.6685-1.70480.16581430.12152715X-RAY DIFFRACTION99
1.7048-1.74440.1681390.12412644X-RAY DIFFRACTION100
1.7444-1.78810.15181430.11482709X-RAY DIFFRACTION100
1.7881-1.83640.15631410.11332681X-RAY DIFFRACTION100
1.8364-1.89040.14551430.10642730X-RAY DIFFRACTION100
1.8904-1.95150.14531420.10562683X-RAY DIFFRACTION100
1.9515-2.02120.13031430.10362727X-RAY DIFFRACTION100
2.0212-2.10210.14351420.10162705X-RAY DIFFRACTION100
2.1021-2.19780.11061420.10372692X-RAY DIFFRACTION100
2.1978-2.31370.13111420.10552693X-RAY DIFFRACTION100
2.3137-2.45860.12581430.1132720X-RAY DIFFRACTION100
2.4586-2.64840.13381430.11882713X-RAY DIFFRACTION100
2.6484-2.91490.15041430.12992724X-RAY DIFFRACTION100
2.9149-3.33660.16021420.14012692X-RAY DIFFRACTION100
3.3366-4.20320.13381450.13972751X-RAY DIFFRACTION100
4.2032-44.34930.18761460.16622766X-RAY DIFFRACTION99

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