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- PDB-4q8p: tRNA-Guanine Transglycosylase (TGT) Mutant V262D in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4q8p
TitletRNA-Guanine Transglycosylase (TGT) Mutant V262D 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: 1.45 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)43,7576
Polymers43,0861
Non-polymers6715
Water5,747319
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,51412
Polymers86,1722
Non-polymers1,34210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4550 Å2
ΔGint-16 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.430, 64.980, 70.360
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

21A-765-

HOH

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Components

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


Mass: 43085.785 Da / Num. of mol.: 1 / Mutation: V262D
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-V262D / 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.: 3 / 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.: 319 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 10% DMSO, 8% PEG 8000, pH 8.5, 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: Apr 26, 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: 1.45→25.3 Å / Num. obs: 72559 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.9 / Num. unique all: 10548 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.45→23.321 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 14.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 3656 5.04 %Random
Rwork0.1375 ---
obs0.1389 72536 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→23.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 43 319 3195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062990
X-RAY DIFFRACTIONf_angle_d1.0084042
X-RAY DIFFRACTIONf_dihedral_angle_d12.2751134
X-RAY DIFFRACTIONf_chiral_restr0.067425
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46910.24361420.1932640X-RAY DIFFRACTION100
1.4691-1.48920.21771280.17722632X-RAY DIFFRACTION100
1.4892-1.51050.22181580.16292649X-RAY DIFFRACTION100
1.5105-1.5330.20291480.1492613X-RAY DIFFRACTION100
1.533-1.5570.17871360.14372646X-RAY DIFFRACTION100
1.557-1.58250.19731470.13972609X-RAY DIFFRACTION100
1.5825-1.60980.16821510.13222640X-RAY DIFFRACTION100
1.6098-1.6390.14841310.12722665X-RAY DIFFRACTION100
1.639-1.67050.16831430.1272599X-RAY DIFFRACTION100
1.6705-1.70460.17131430.12182671X-RAY DIFFRACTION100
1.7046-1.74170.1621350.12172644X-RAY DIFFRACTION100
1.7417-1.78220.16311430.12092609X-RAY DIFFRACTION100
1.7822-1.82670.17781240.11552687X-RAY DIFFRACTION100
1.8267-1.87610.14631130.1162673X-RAY DIFFRACTION100
1.8761-1.93130.14311220.11692654X-RAY DIFFRACTION100
1.9313-1.99360.15271440.11942669X-RAY DIFFRACTION100
1.9936-2.06480.15681420.12282624X-RAY DIFFRACTION100
2.0648-2.14740.13681410.12192653X-RAY DIFFRACTION100
2.1474-2.24510.17041400.12692655X-RAY DIFFRACTION100
2.2451-2.36330.1711330.13212628X-RAY DIFFRACTION100
2.3633-2.51130.18221590.1412671X-RAY DIFFRACTION100
2.5113-2.70490.16171430.14692658X-RAY DIFFRACTION100
2.7049-2.97660.18471520.1482646X-RAY DIFFRACTION100
2.9766-3.40620.1571440.14582660X-RAY DIFFRACTION100
3.4062-4.28710.1431580.13282676X-RAY DIFFRACTION100
4.2871-23.32440.16481360.16112709X-RAY DIFFRACTION99

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