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- PDB-7a4k: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a4k
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with tetramethylene sulfoxide
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / enzyme / disulfide / fragment
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
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
thiolane 1-oxide / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsNguyen, D. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)324043133 Germany
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface.
Authors: Nguyen, D. / Xie, X. / Jakobi, S. / Terwesten, F. / Metz, A. / Nguyen, T.X.P. / Palchykov, V.A. / Heine, A. / Reuter, K. / Klebe, G.
History
DepositionAug 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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)43,3566
Polymers42,9111
Non-polymers4465
Water4,990277
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,71312
Polymers85,8212
Non-polymers89210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2580 Å2
ΔGint-15 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.270, 128.270, 114.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

21A-756-

HOH

31A-772-

HOH

41A-774-

HOH

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Components

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


Mass: 42910.605 Da / Num. of mol.: 1 / Mutation: C158S/C281S/Y330C/H333A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: Escherichia coli BL21(DE3) (bacteria)
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-QZT / thiolane 1-oxide


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.18 Å3/Da / Density % sol: 61.34 % / Description: hexagonal bipyramidal
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 4% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.68→42.81 Å / Num. obs: 63158 / % possible obs: 98.9 % / Redundancy: 15.6 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 1 / Rsym value: 0.068 / Net I/σ(I): 25.9
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10078 / CC1/2: 0.615 / Rsym value: 1.749 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.68→42.81 Å / SU ML: 0.1704 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1899 3158 5 %
Rwork0.1553 59997 -
obs0.1571 63155 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.33 Å2
Refinement stepCycle: LAST / Resolution: 1.68→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 25 277 3195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833138
X-RAY DIFFRACTIONf_angle_d0.92654252
X-RAY DIFFRACTIONf_chiral_restr0.0498446
X-RAY DIFFRACTIONf_plane_restr0.0065577
X-RAY DIFFRACTIONf_dihedral_angle_d15.24141903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.35441330.26952541X-RAY DIFFRACTION97.52
1.7-1.730.27741360.23752579X-RAY DIFFRACTION99.85
1.73-1.760.24781370.20522594X-RAY DIFFRACTION99.78
1.76-1.790.26271350.20372568X-RAY DIFFRACTION99.89
1.79-1.820.2581370.18662611X-RAY DIFFRACTION99.85
1.82-1.860.18721370.18672600X-RAY DIFFRACTION99.56
1.86-1.90.21951360.16432583X-RAY DIFFRACTION99.49
1.9-1.940.20921370.16092606X-RAY DIFFRACTION99.71
1.94-1.980.20811360.15232583X-RAY DIFFRACTION99.49
1.98-2.030.19071360.13962590X-RAY DIFFRACTION99.67
2.03-2.090.19391370.14222597X-RAY DIFFRACTION99.6
2.09-2.150.18411370.13472598X-RAY DIFFRACTION99.35
2.15-2.220.19511370.13472614X-RAY DIFFRACTION99.24
2.22-2.30.15491370.12512595X-RAY DIFFRACTION99.31
2.3-2.390.15061370.12572607X-RAY DIFFRACTION99.24
2.39-2.50.17321380.13162611X-RAY DIFFRACTION98.99
2.5-2.630.17981370.14422600X-RAY DIFFRACTION98.92
2.63-2.790.20511370.14752604X-RAY DIFFRACTION98.46
2.79-3.010.18851380.15672620X-RAY DIFFRACTION98.43
3.01-3.310.18731380.15432628X-RAY DIFFRACTION98.19
3.31-3.790.16981380.1442635X-RAY DIFFRACTION97.92
3.79-4.770.16221410.14032665X-RAY DIFFRACTION97.33

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