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- PDB-7a3x: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a3x
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with sulfolane
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
sulfolane / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jun 30, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.oper_expression
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 13, 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)43,5217
Polymers42,9111
Non-polymers6106
Water3,207178
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,04114
Polymers85,8212
Non-polymers1,22012
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation6_554x-y,x,z-1/61
crystal symmetry operation7_554y,x,-z-1/31
Buried area1620 Å2
ΔGint-12 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.292, 128.292, 114.859
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-675-

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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-QXB / sulfolane / thiolane 1,1-dioxide


Mass: 120.170 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 61.31 % / 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: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.85→42.8 Å / Num. obs: 47943 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 31.52 Å2 / CC1/2: 0.998 / Rsym value: 0.111 / Net I/σ(I): 12.8
Reflection shellResolution: 1.85→2.05 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7607 / CC1/2: 0.611 / Rsym value: 1.604 / % possible all: 99.9

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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: 1.85→42.79 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2257 2398 5 %
Rwork0.2028 45541 -
obs0.204 47939 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.96 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 34 178 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662896
X-RAY DIFFRACTIONf_angle_d0.79433925
X-RAY DIFFRACTIONf_chiral_restr0.0513416
X-RAY DIFFRACTIONf_plane_restr0.0055525
X-RAY DIFFRACTIONf_dihedral_angle_d13.79851741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.32581390.30792629X-RAY DIFFRACTION99.6
1.89-1.930.28431380.27072622X-RAY DIFFRACTION99.96
1.93-1.970.27961390.24672644X-RAY DIFFRACTION100
1.97-2.020.27871390.23892647X-RAY DIFFRACTION100
2.02-2.080.2581390.22362632X-RAY DIFFRACTION100
2.08-2.140.25431400.21232655X-RAY DIFFRACTION99.96
2.14-2.210.23531380.19952630X-RAY DIFFRACTION99.39
2.21-2.290.24841390.19542645X-RAY DIFFRACTION100
2.29-2.380.23251390.18712645X-RAY DIFFRACTION100
2.38-2.490.2121410.19372669X-RAY DIFFRACTION100
2.49-2.620.22051410.18882676X-RAY DIFFRACTION99.96
2.62-2.780.22061400.19852672X-RAY DIFFRACTION99.75
2.78-30.2191410.19282663X-RAY DIFFRACTION99.64
3-3.30.20081420.19082716X-RAY DIFFRACTION99.97
3.3-3.770.21091440.19112727X-RAY DIFFRACTION100
3.77-4.750.2011450.18322751X-RAY DIFFRACTION99.66
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)
10.9550294198330.5000895321470.4120386523581.100328461870.1647089013820.6278692696160.0996664713981-0.05949323248480.2350871959180.0933341180028-0.0817701727397-0.0619218484338-0.1576111724640.00606553462573-0.00148615050650.316181758547-0.0260176551176-0.01799849685170.2425237152-0.04425633041050.31762939768216.322046939546.5892251919-2.30709295854
21.195929951710.1437326735980.3469549155920.7796657366930.04371745179570.460468686090.136702261866-0.2060501922110.09296553476660.0404473077763-0.1478504224620.267127051129-0.0174105429598-0.1622777277720.009016629590650.24701418642-0.0053352129484-0.01726546272270.297745255648-0.02051937433740.2308719402793.5055127899931.2793116867-1.91973018176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 207 )
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 383 )

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