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- PDB-4q8w: tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amin... -

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Basic information

Entry
Database: PDB / ID: 4q8w
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzoic acid
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/transferase inhibitor / Guanine Exchange Enzyme / preQ1 / tRNA / Transferase-transferase inhibitor complex
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-2YY / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Addressing a New Subpocket of TGT by Elongated 2-Amino-lin-benzoguanines
Authors: Neeb, M. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,8687
Polymers43,0701
Non-polymers7986
Water6,774376
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,73614
Polymers86,1402
Non-polymers1,59612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area5100 Å2
ΔGint-16 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.830, 64.680, 70.680
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

21A-668-

HOH

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Components

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


Mass: 43069.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2-ZM-WT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
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-2YY / 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoic acid


Mass: 364.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N6O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: ...AUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288 (1995). THE CORRECT RESIDUE IS A LYS

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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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97627 Å
DetectorType: PILATUS / Detector: PIXEL / Date: Nov 14, 2013
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.14→80 Å / Num. obs: 134549 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.028 / Net I/σ(I): 27.8
Reflection shellResolution: 1.14→1.19 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 15089 / Rsym value: 0.309 / % possible all: 80

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.14→70.257 Å / SU ML: 0.08 / Cross valid method: R-free / σ(F): 1.36 / Phase error: 13.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1496 6728 5 %Random
Rwork0.1343 ---
obs0.1351 134534 92.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→70.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 52 376 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063055
X-RAY DIFFRACTIONf_angle_d1.1694130
X-RAY DIFFRACTIONf_dihedral_angle_d12.8921156
X-RAY DIFFRACTIONf_chiral_restr0.071434
X-RAY DIFFRACTIONf_plane_restr0.006545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.15290.19951590.18583018X-RAY DIFFRACTION65
1.1529-1.16650.19841870.17393549X-RAY DIFFRACTION78
1.1665-1.18070.18142160.16364107X-RAY DIFFRACTION89
1.1807-1.19570.17592170.1564127X-RAY DIFFRACTION89
1.1957-1.21140.17522180.14654141X-RAY DIFFRACTION89
1.2114-1.2280.15372190.14114148X-RAY DIFFRACTION90
1.228-1.24550.152180.13374154X-RAY DIFFRACTION90
1.2455-1.26410.15852210.13214203X-RAY DIFFRACTION91
1.2641-1.28390.13342220.12654215X-RAY DIFFRACTION91
1.2839-1.30490.14682210.12214187X-RAY DIFFRACTION92
1.3049-1.32740.1362240.12074265X-RAY DIFFRACTION92
1.3274-1.35160.13652290.11744335X-RAY DIFFRACTION93
1.3516-1.37760.14272230.11534249X-RAY DIFFRACTION93
1.3776-1.40570.13332270.11264301X-RAY DIFFRACTION93
1.4057-1.43630.1512240.10884275X-RAY DIFFRACTION93
1.4363-1.46970.12912270.10564300X-RAY DIFFRACTION93
1.4697-1.50640.12112290.10334361X-RAY DIFFRACTION94
1.5064-1.54720.12932280.09994330X-RAY DIFFRACTION94
1.5472-1.59270.11652300.09834359X-RAY DIFFRACTION94
1.5927-1.64410.11762300.10414383X-RAY DIFFRACTION95
1.6441-1.70290.13462310.1094384X-RAY DIFFRACTION95
1.7029-1.77110.11832320.1144403X-RAY DIFFRACTION95
1.7711-1.85170.12862330.11754420X-RAY DIFFRACTION95
1.8517-1.94930.14422350.12534465X-RAY DIFFRACTION96
1.9493-2.07140.16052340.12894445X-RAY DIFFRACTION96
2.0714-2.23140.15322360.13134493X-RAY DIFFRACTION97
2.2314-2.45590.16982370.13914502X-RAY DIFFRACTION97
2.4559-2.81130.15752380.15314519X-RAY DIFFRACTION97
2.8113-3.5420.14142390.14674554X-RAY DIFFRACTION97
3.542-70.39030.16942440.15664614X-RAY DIFFRACTION97

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