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- PDB-7a6d: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a6d
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with rac-trans-4,4-difluorocyclopentane-1,2-diol
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / enzyme / disulfide / fragment
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
: / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase
Similarity search - Domain/homology
trans-4,4-difluorocyclopentane-1,2-diol / Chem-RGN / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 25, 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 1.4Oct 23, 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

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6539
Polymers42,9111
Non-polymers7428
Water4,702261
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30518
Polymers85,8212
Non-polymers1,48416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3000 Å2
ΔGint-2 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.868, 127.868, 115.189
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-408-

RGN

21A-747-

HOH

31A-759-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 269 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-R1E / trans-4,4-difluorocyclopentane-1,2-diol / (1~{S},2~{S})-4,4-bis(fluoranyl)cyclopentane-1,2-diol


Mass: 138.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8F2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-RGN / (1~{R},2~{R})-4,4-bis(fluoranyl)cyclopentane-1,2-diol


Mass: 138.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H8F2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.17 % / 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: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.59→42.79 Å / Num. obs: 74885 / % possible obs: 99.8 % / Redundancy: 17.5 % / Biso Wilson estimate: 25.05 Å2 / CC1/2: 1 / Rsym value: 0.08 / Net I/σ(I): 21.7
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11815 / CC1/2: 0.609 / Rsym value: 2.058 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Coot0.8.9-premodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.59→42.79 Å / SU ML: 0.1447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1775 3739 5 %
Rwork0.1481 71023 -
obs0.1496 74762 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.09 Å2
Refinement stepCycle: LAST / Resolution: 1.59→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 45 261 3137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843089
X-RAY DIFFRACTIONf_angle_d0.96424184
X-RAY DIFFRACTIONf_chiral_restr0.0547441
X-RAY DIFFRACTIONf_plane_restr0.0065561
X-RAY DIFFRACTIONf_dihedral_angle_d16.82881867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.2841310.25262482X-RAY DIFFRACTION96.03
1.61-1.630.32531360.23712595X-RAY DIFFRACTION100
1.63-1.650.24461370.21622588X-RAY DIFFRACTION99.96
1.65-1.680.23921360.2052593X-RAY DIFFRACTION100
1.68-1.70.21531380.19642614X-RAY DIFFRACTION100
1.7-1.730.23691360.1832587X-RAY DIFFRACTION99.96
1.73-1.760.20691370.16652601X-RAY DIFFRACTION100
1.76-1.790.19641360.16512590X-RAY DIFFRACTION100
1.79-1.820.19211370.15632595X-RAY DIFFRACTION100
1.82-1.850.21971380.15322624X-RAY DIFFRACTION100
1.85-1.890.20281370.14322608X-RAY DIFFRACTION100
1.89-1.930.16871360.14392593X-RAY DIFFRACTION100
1.93-1.980.19391380.13382616X-RAY DIFFRACTION100
1.98-2.030.17751380.13232622X-RAY DIFFRACTION100
2.03-2.080.15681370.13262594X-RAY DIFFRACTION99.96
2.08-2.140.17961380.13042624X-RAY DIFFRACTION100
2.14-2.210.16281390.1282636X-RAY DIFFRACTION100
2.21-2.290.15551380.12452623X-RAY DIFFRACTION100
2.29-2.380.15781380.1232635X-RAY DIFFRACTION100
2.38-2.490.14851390.12672627X-RAY DIFFRACTION100
2.49-2.620.16761390.13552643X-RAY DIFFRACTION100
2.62-2.790.18881390.13882651X-RAY DIFFRACTION100
2.79-30.1721400.152661X-RAY DIFFRACTION100
3-3.30.17151420.14712686X-RAY DIFFRACTION100
3.3-3.780.17061410.14322694X-RAY DIFFRACTION100
3.78-4.760.14531450.13292744X-RAY DIFFRACTION100

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