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- PDB-4q8q: tRNA-Guanine Transglycosylase (TGT) Mutant V262C in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4q8q
TitletRNA-Guanine Transglycosylase (TGT) Mutant V262C 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 / 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
Chem-CKR / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.721 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,4693
Polymers43,0741
Non-polymers3952
Water5,278293
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9376
Polymers86,1482
Non-polymers7904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-20 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.438, 65.035, 70.259
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-793-

HOH

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Components

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


Mass: 43073.840 Da / Num. of mol.: 1 / Mutation: V262C
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-V262C / 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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: May 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: 1.72→30 Å / Num. obs: 37958 / % possible obs: 87.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.099 / Net I/σ(I): 9.4
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1991 / Rsym value: 0.374 / % possible all: 91

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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: 1.721→29.482 Å / SU ML: 0.15 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1898 5 %Random
Rwork0.1732 ---
obs0.1748 37947 87.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.721→29.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 18 293 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072844
X-RAY DIFFRACTIONf_angle_d1.0733830
X-RAY DIFFRACTIONf_dihedral_angle_d13.8511039
X-RAY DIFFRACTIONf_chiral_restr0.042404
X-RAY DIFFRACTIONf_plane_restr0.005505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7213-1.76430.23281370.21452588X-RAY DIFFRACTION88
1.7643-1.8120.21791390.19012656X-RAY DIFFRACTION91
1.812-1.86530.20511400.1852660X-RAY DIFFRACTION91
1.8653-1.92550.22531390.17612631X-RAY DIFFRACTION90
1.9255-1.99430.21541380.17552645X-RAY DIFFRACTION89
1.9943-2.07420.21861390.16662622X-RAY DIFFRACTION89
2.0742-2.16850.1991360.16642591X-RAY DIFFRACTION89
2.1685-2.28280.19511360.16372585X-RAY DIFFRACTION88
2.2828-2.42580.19151360.16762573X-RAY DIFFRACTION87
2.4258-2.6130.21411340.1722550X-RAY DIFFRACTION87
2.613-2.87570.221340.18052530X-RAY DIFFRACTION86
2.8757-3.29140.21251330.17922527X-RAY DIFFRACTION85
3.2914-4.1450.18981290.16472465X-RAY DIFFRACTION83
4.145-29.48620.19161280.17012426X-RAY DIFFRACTION80
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)
11.62130.36120.31110.41570.03660.79390.0385-0.0659-0.0980.0023-0.0202-0.0020.0213-0.0759-0.0140.1281-0.00370.00720.11240.00520.1516-13.93760.256-16.4567
21.2202-0.08280.84420.743-0.60461.1077-0.10120.04210.18960.09390.0018-0.0028-0.25310.05640.08160.14470.00330.00870.1255-0.00660.1629-6.107916.5046-24.1964
31.30580.1375-0.18351.5527-0.37391.30450.01360.10460.0893-0.00380.05230.1281-0.0796-0.0862-0.07210.0978-0.0028-0.00450.120.00840.1161-21.97213.3839-28.4447
40.84090.53731.17150.35330.76811.663-0.0091-0.1150.03870.0374-0.02250.0689-0.014-0.12530.04710.1220.00550.01120.14810.00580.1687-19.03077.17620.3294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 264 )
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 383 )

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