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- PDB-4q4m: tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-4-phe... -

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Basic information

Entry
Database: PDB / ID: 4q4m
TitletRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-4-phenyl-1,2-dihydro-1,3,5-triazin-2-one
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/transferase inhibitor / Transferase / preQ1 / tRNA / Guanine Exchange Enzyme / 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
6-amino-4-phenyl-1,3,5-triazin-2(1H)-one / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.621 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: 5-Azacytosines as a Novel Scaffold to Inhibit Z. mobilis TGT with Expected Improved Bioavailability and Synthetic Accessibility
Authors: Neeb, M. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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)43,4927
Polymers42,9261
Non-polymers5666
Water6,107339
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98414
Polymers85,8512
Non-polymers1,13212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area4580 Å2
ΔGint-5 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.511, 63.887, 70.399
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme
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: pET9d-ZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
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-2YL / 6-amino-4-phenyl-1,3,5-triazin-2(1H)-one


Mass: 188.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N4O
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; ...AUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995).

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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: 2.32 Å3/Da / Density % sol: 46.87 %
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: BESSY / Beamline: 14.3 / Wavelength: 0.8946 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2012 / Details: Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8946 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. obs: 48799 / % possible obs: 98 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.05 / Net I/σ(I): 21.5
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2059 / Rsym value: 0.3 / % possible all: 82.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.621→26.837 Å / SU ML: 0.13 / Cross valid method: R-free / σ(F): 1.37 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2466 5.05 %Random
Rwork0.157 ---
obs0.1586 48795 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.621→26.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 31 339 3181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062943
X-RAY DIFFRACTIONf_angle_d1.0683976
X-RAY DIFFRACTIONf_dihedral_angle_d12.751091
X-RAY DIFFRACTIONf_chiral_restr0.042419
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6209-1.65210.2991040.21532189X-RAY DIFFRACTION82
1.6521-1.68580.22811240.18612571X-RAY DIFFRACTION100
1.6858-1.72240.22821370.18072626X-RAY DIFFRACTION100
1.7224-1.76250.22751520.17462623X-RAY DIFFRACTION100
1.7625-1.80650.18411300.16482602X-RAY DIFFRACTION100
1.8065-1.85540.20571530.15432611X-RAY DIFFRACTION100
1.8554-1.910.18831230.15162594X-RAY DIFFRACTION100
1.91-1.97160.18891410.14452613X-RAY DIFFRACTION100
1.9716-2.0420.15331400.15312602X-RAY DIFFRACTION100
2.042-2.12380.19121350.15032646X-RAY DIFFRACTION100
2.1238-2.22040.17661490.15172582X-RAY DIFFRACTION99
2.2204-2.33740.18431350.1432608X-RAY DIFFRACTION99
2.3374-2.48370.16371540.15212596X-RAY DIFFRACTION99
2.4837-2.67530.16861460.15382568X-RAY DIFFRACTION99
2.6753-2.94430.1981400.15992591X-RAY DIFFRACTION98
2.9443-3.36960.21471280.15842597X-RAY DIFFRACTION98
3.3696-4.24260.17241350.14992571X-RAY DIFFRACTION97
4.2426-26.84070.18921400.16142539X-RAY DIFFRACTION94
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)
12.727-0.61640.70640.6561-0.23021.8662-0.0270.0274-0.07910.05660.0422-0.00670.04420.0636-0.01920.07880.00350.00190.052-0.01210.0735102.03121.078516.7156
21.196-0.08-0.120.49910.15771.09160.0125-0.10810.21730.02280.0314-0.0972-0.19660.1068-0.03220.1398-0.0086-0.00670.1062-0.01110.1399103.188914.492326.1812
30.8769-0.45931.21360.479-0.78691.9038-0.00970.12740.0323-0.0457-0.054-0.0704-0.0120.19250.06720.089-0.00890.01250.12870.00310.108106.23677.835-0.7852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 383 )

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