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- PDB-4q8o: tRNA-Guanine Transglycosylase (TGT) Mutant V262T in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4q8o
TitletRNA-Guanine Transglycosylase (TGT) Mutant V262T in Complex with 6-Amino-2-{[2-(morpholin-4-yl)ethyl]amino}-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one
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 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-CKR / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.887 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Creating a Resistance Model for TGT: The Effect of Mutations on Flexible lin-Benzoguanine Substituents
Authors: Neeb, M. / Heine, A. / 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_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)43,8357
Polymers43,0721
Non-polymers7636
Water4,558253
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,67014
Polymers86,1442
Non-polymers1,52612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5380 Å2
ΔGint-19 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.327, 64.858, 71.371
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-605-

HOH

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Components

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


Mass: 43071.801 Da / Num. of mol.: 1 / Mutation: V262T
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-V262T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus(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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CKR / 6-amino-2-[(2-morpholin-4-ylethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one / 6-Amino-2-[(2-morpholin-4-ylethyl)amino]-8-oxo-7,8-dihydro-1H-imidazo[4,5-G]quinazolin


Mass: 329.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N7O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
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: Mar 16, 2012 / 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: 1.89→30 Å / Num. obs: 32679 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.1 Å2 / Rsym value: 0.079 / Net I/σ(I): 15.1
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1625 / Rsym value: 0.434 / % possible all: 96.3

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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: 1.887→23.631 Å / SU ML: 0.17 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1650 5.05 %Random
Rwork0.1561 ---
obs0.1579 32654 97.68 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.887→23.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 49 253 3125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082953
X-RAY DIFFRACTIONf_angle_d1.053979
X-RAY DIFFRACTIONf_dihedral_angle_d12.6951110
X-RAY DIFFRACTIONf_chiral_restr0.041420
X-RAY DIFFRACTIONf_plane_restr0.006543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8869-1.94240.26361440.22682466X-RAY DIFFRACTION95
1.9424-2.00510.231250.1822601X-RAY DIFFRACTION97
2.0051-2.07670.23321170.16922540X-RAY DIFFRACTION97
2.0767-2.15980.18371310.15212579X-RAY DIFFRACTION97
2.1598-2.2580.22791380.15542553X-RAY DIFFRACTION97
2.258-2.37690.21251430.15552551X-RAY DIFFRACTION98
2.3769-2.52570.18271370.15782592X-RAY DIFFRACTION98
2.5257-2.72050.19671590.16062569X-RAY DIFFRACTION98
2.7205-2.99370.18551310.16212621X-RAY DIFFRACTION98
2.9937-3.42580.18681420.15532612X-RAY DIFFRACTION99
3.4258-4.31190.14971530.1392636X-RAY DIFFRACTION99
4.3119-23.63280.19231300.14942684X-RAY DIFFRACTION99
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)
11.18260.5810.21510.3728-0.02920.9263-0.01210.08640.0576-0.04820.02890.0477-0.06920.0134-0.02170.14090.0044-0.00990.1103-0.00250.1508-8.86357.2252-18.8683
21.16530.0595-0.35620.8826-0.3841.31710.01570.15030.1041-0.06920.03870.0779-0.1183-0.0523-0.05780.191-0.0145-0.04030.16830.00530.1556-18.75114.6537-27.731
31.7170.86122.12591.04551.43652.9683-0.0291-0.12470.0390.0143-0.03940.07460.0035-0.18680.06490.15140.01460.00460.13950.0170.1536-17.78667.88370.885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 383 )

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