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- PDB-4q8u: tRNA-Guanine Transglycosylase (TGT) in Complex with Methyl 4-[2-(... -

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Basic information

Entry
Database: PDB / ID: 4q8u
TitletRNA-Guanine Transglycosylase (TGT) in Complex with Methyl 4-[2-({6-amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzoate
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTransferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / preQ1 / tRNA / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) 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-2YW / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 1.1Sep 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)44,01410
Polymers42,9261
Non-polymers1,0889
Water5,945330
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,02820
Polymers85,8512
Non-polymers2,17718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6640 Å2
ΔGint-17 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.751, 64.490, 70.896
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-642-

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
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2YW / methyl 4-{2-[(6-amino-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-2-yl)amino]ethyl}benzoate


Mass: 378.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2013 / Details: Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.31→30 Å / Num. obs: 96126 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 21.8
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 4340 / Rsym value: 0.474 / % possible all: 89.9

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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: pdb entry 1PUD

1pud


Resolution: 1.31→18.101 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 4814 5.01 %Random
Rwork0.1402 ---
obs0.1413 96103 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→18.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 71 330 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063036
X-RAY DIFFRACTIONf_angle_d1.1894109
X-RAY DIFFRACTIONf_dihedral_angle_d12.8241137
X-RAY DIFFRACTIONf_chiral_restr0.07432
X-RAY DIFFRACTIONf_plane_restr0.006539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3104-1.32530.22361590.22922798X-RAY DIFFRACTION93
1.3253-1.34090.22721550.21233052X-RAY DIFFRACTION100
1.3409-1.35720.23011320.21033058X-RAY DIFFRACTION100
1.3572-1.37440.23911710.19113067X-RAY DIFFRACTION100
1.3744-1.39250.22291570.18193060X-RAY DIFFRACTION100
1.3925-1.41160.2271600.17113044X-RAY DIFFRACTION100
1.4116-1.43170.18021730.163012X-RAY DIFFRACTION100
1.4317-1.45310.17781600.15113088X-RAY DIFFRACTION100
1.4531-1.47580.15411520.13683004X-RAY DIFFRACTION100
1.4758-1.50.16991730.1283097X-RAY DIFFRACTION100
1.5-1.52580.14821560.12263053X-RAY DIFFRACTION100
1.5258-1.55350.15641460.1183019X-RAY DIFFRACTION100
1.5535-1.58340.13741480.10943098X-RAY DIFFRACTION100
1.5834-1.61570.14131710.10743046X-RAY DIFFRACTION100
1.6157-1.65080.13921540.10353057X-RAY DIFFRACTION100
1.6508-1.68920.12451460.10513105X-RAY DIFFRACTION100
1.6892-1.73140.13861690.10733030X-RAY DIFFRACTION100
1.7314-1.77820.12911700.10913045X-RAY DIFFRACTION100
1.7782-1.83050.15731470.11123087X-RAY DIFFRACTION100
1.8305-1.88950.13771640.11553036X-RAY DIFFRACTION100
1.8895-1.95690.13251760.11663058X-RAY DIFFRACTION100
1.9569-2.03520.1411700.11763052X-RAY DIFFRACTION100
2.0352-2.12770.14961640.11673067X-RAY DIFFRACTION100
2.1277-2.23970.14431600.12733078X-RAY DIFFRACTION100
2.2397-2.37970.14221590.1323065X-RAY DIFFRACTION100
2.3797-2.5630.15511630.1463059X-RAY DIFFRACTION100
2.563-2.820.18211720.15043082X-RAY DIFFRACTION100
2.82-3.22610.16671720.15073092X-RAY DIFFRACTION100
3.2261-4.0570.16741680.14373057X-RAY DIFFRACTION99
4.057-18.10270.18151470.17142823X-RAY DIFFRACTION89

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