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- PDB-7a0b: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a0b
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with rac-trans-3,4-dihydroxysulfolane
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
Chem-QTQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 7, 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 16, 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)43,7119
Polymers42,9111
Non-polymers8008
Water3,279182
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42218
Polymers85,8212
Non-polymers1,60016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3300 Å2
ΔGint-10 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.860, 127.860, 115.735
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-681-

HOH

21A-682-

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 , 5 types, 190 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-QTQ / (3~{R},4~{R})-1,1-bis(oxidanylidene)thiolane-3,4-diol


Mass: 152.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.18 Å3/Da / Density % sol: 61.35 % / 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: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.77→42.9 Å / Num. obs: 54711 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Rsym value: 0.082 / Net I/σ(I): 17.9
Reflection shellResolution: 1.77→1.88 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8690 / CC1/2: 0.613 / Rsym value: 1.528 / % possible all: 99.8

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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: 1.77→42.9 Å / SU ML: 0.1889 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 2736 5 %
Rwork0.1835 51974 -
obs0.1844 54710 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.89 Å2
Refinement stepCycle: LAST / Resolution: 1.77→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 47 182 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663052
X-RAY DIFFRACTIONf_angle_d0.78224132
X-RAY DIFFRACTIONf_chiral_restr0.053440
X-RAY DIFFRACTIONf_plane_restr0.0057550
X-RAY DIFFRACTIONf_dihedral_angle_d16.50971834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.30761340.29082553X-RAY DIFFRACTION99.41
1.8-1.830.27231340.26042539X-RAY DIFFRACTION100
1.83-1.870.26921340.2482551X-RAY DIFFRACTION100
1.87-1.910.26791350.2362564X-RAY DIFFRACTION99.96
1.91-1.950.25461340.21582547X-RAY DIFFRACTION99.96
1.95-1.990.23791350.2112560X-RAY DIFFRACTION99.96
1.99-2.040.24831350.19062564X-RAY DIFFRACTION100
2.04-2.10.23181360.18822582X-RAY DIFFRACTION100
2.1-2.160.22171350.17922560X-RAY DIFFRACTION100
2.16-2.230.2281360.17712582X-RAY DIFFRACTION100
2.23-2.310.21711350.18082576X-RAY DIFFRACTION100
2.31-2.40.17711360.1762591X-RAY DIFFRACTION100
2.4-2.510.211360.18582577X-RAY DIFFRACTION100
2.51-2.640.18241370.18122599X-RAY DIFFRACTION99.89
2.64-2.810.22221370.18252605X-RAY DIFFRACTION100
2.81-3.030.21861380.18632617X-RAY DIFFRACTION99.96
3.03-3.330.19231380.17492626X-RAY DIFFRACTION100
3.33-3.810.15991390.16562640X-RAY DIFFRACTION99.89
3.81-4.80.16731420.15832695X-RAY DIFFRACTION99.96
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)
11.124380594480.7731610851330.5721506039811.162251779810.3900297926580.8764205081710.138549141922-0.1473262580530.1322785725980.123314419621-0.182093291329-0.0773454723398-0.164418575006-0.0741690663133-0.008129159293060.329447899724-0.0413418117855-0.04698726791940.23374595519-0.03977326970170.25248485463815.102199132646.8347098164-0.715557537253
21.14921274041-0.1602017163470.2803215384630.4624085796770.05291960839570.619952292240.149846553305-0.228279779047-0.1113255715750.0438385926824-0.1835703182630.1789887538940.0175131067335-0.1979374336150.001141043242130.233753183742-0.0420257535707-0.0464060909050.305786947473-0.00097640767040.2401730689362.8973193930427.5621135818-3.58302131323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 236 )
2X-RAY DIFFRACTION2chain 'A' and (resid 237 through 386 )

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