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- PDB-7a3v: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a3v
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with 3-hydroxysulfolane
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
3-hydroxythietane-1,1-dioxide / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2.0Jun 23, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 2.1Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jan 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 2.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4957
Polymers42,9111
Non-polymers5846
Water3,801211
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,98914
Polymers85,8212
Non-polymers1,16812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2240 Å2
ΔGint-7 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.959, 127.959, 115.518
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-655-

HOH

21A-703-

HOH

31A-710-

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 ZM4 = ATCC 31821 (bacteria)
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, 217 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-QXE / 3-hydroxythietane-1,1-dioxide / (3~{R})-1,1-bis(oxidanylidene)thiolan-3-ol


Mass: 136.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O3S / 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.: 211 / 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: 3.31 Å3/Da / Density % sol: 62.83 % / 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: 1.7→42.87 Å / Num. obs: 61476 / % possible obs: 99.7 % / Redundancy: 17.1 % / Biso Wilson estimate: 27.03 Å2 / CC1/2: 0.998 / Rsym value: 0.124 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9767 / CC1/2: 0.6 / Rsym value: 1.641 / % possible all: 98.4

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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: 1.7→42.87 Å / SU ML: 0.1691 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2003 3065 5 %
Rwork0.1808 58225 -
obs0.1817 61290 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.49 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 33 211 3037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653018
X-RAY DIFFRACTIONf_angle_d0.7934089
X-RAY DIFFRACTIONf_chiral_restr0.0535435
X-RAY DIFFRACTIONf_plane_restr0.0058547
X-RAY DIFFRACTIONf_dihedral_angle_d16.29631817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.29461320.29052501X-RAY DIFFRACTION95.64
1.73-1.760.30891350.262567X-RAY DIFFRACTION98.54
1.76-1.790.28531360.24342595X-RAY DIFFRACTION100
1.79-1.820.24171380.22182607X-RAY DIFFRACTION100
1.82-1.850.25151380.2092632X-RAY DIFFRACTION100
1.85-1.890.21251380.19982612X-RAY DIFFRACTION100
1.89-1.930.21921370.18932615X-RAY DIFFRACTION100
1.93-1.980.21161390.17932632X-RAY DIFFRACTION100
1.98-2.030.19941380.16862621X-RAY DIFFRACTION99.96
2.03-2.080.18211380.16672619X-RAY DIFFRACTION100
2.08-2.140.1911380.16322634X-RAY DIFFRACTION100
2.14-2.210.18031390.15932646X-RAY DIFFRACTION100
2.21-2.290.17111380.16422621X-RAY DIFFRACTION100
2.29-2.380.19721400.16752653X-RAY DIFFRACTION100
2.38-2.490.20621390.18182633X-RAY DIFFRACTION100
2.49-2.620.20941390.17952655X-RAY DIFFRACTION100
2.62-2.790.18251400.1772664X-RAY DIFFRACTION99.96
2.79-30.17491410.18682668X-RAY DIFFRACTION99.93
3-3.30.2041420.17262692X-RAY DIFFRACTION99.89
3.3-3.780.18821420.16362704X-RAY DIFFRACTION100
3.78-4.760.15481450.16812749X-RAY DIFFRACTION99.9
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)
10.200577825690.02347034803190.09847262186580.0303630572273-0.02289982605380.0764301653095-0.08586815503180.07943120161850.274662250171-0.19216604305-0.08877160866330.113071802155-0.275199748343-0.1030589193174.55200140348E-50.355520111440.0541211154042-0.05963103619830.274292464932-0.02750773216990.3108629581823.6689317183247.1041606953-13.7376790556
20.1033879600340.1007817266-0.2742421734740.792828662384-0.2222687785450.6013185240760.03432598344450.06940060811270.03649721755430.0429053722611-0.050913609482-0.190691258765-0.1327588111730.101951577987-1.66885526841E-50.271314788702-0.0302043467135-0.06184690111610.230195625871-0.02277399101380.26716440838620.681378746538.2825062875-7.53864074437
30.4976931393240.369169549069-0.09522043877130.388690852457-0.1442427103490.1710933091510.493528770902-0.752491658918-0.1797115500860.936909061393-0.400973303488-0.2401385631240.343829157081-0.007258316446420.0703268405740.65559207575-0.205621635755-0.2383283035740.3320194021230.02234207403820.32451519181925.004759908244.977311941111.7988908051
41.219735842790.4110446643510.7953244095810.9416928776740.2034598344530.6969357226280.198860373534-0.3264011383180.3067668804510.253349533511-0.241274409132-0.151834208065-0.333008568097-0.124254614054-0.1410668816280.426145988389-0.108404229811-0.04797212363460.268679309011-0.09570620834050.29771669382717.608895565552.81245331795.49058466232
51.343525321180.729263521570.6104770952530.6394035248050.4865300073030.9997079614660.147586210322-0.4004935813450.2605397332620.0996780730945-0.2912266202670.145740382794-0.275627013918-0.24811368594-0.003365851356530.3300288787110.017585062641-0.01257873070160.298556676934-0.09744106737640.2967710723913.9831988535248.2927247962.58254448951
61.61268602641-1.17760760770.4755248930660.981400594214-0.05440232975250.5708282799830.152999580298-0.150026547908-0.204574222725-0.017013991932-0.1043947243470.1917307823950.0437095791642-0.1097107844620.0001550735543770.209978073537-0.0277905878409-0.05939704507250.222431905710.0176129338510.2249276711136.7763817640821.6124220521-5.65092913484
70.167918758119-0.0592943477579-0.08449855153290.696342945951-0.08354699739740.1456934456440.11896871842-0.228744663086-0.2230860619480.275217560643-0.1694416442830.94567167262-0.12138080947-0.292972163335-0.01252946918680.237786464872-0.03427622383160.0004330040157680.435810792291-0.06258042481260.407065749922-8.7218815768328.4981234935-3.89355596313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 188 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 274 )
6X-RAY DIFFRACTION6chain 'A' and (resid 275 through 366 )
7X-RAY DIFFRACTION7chain 'A' and (resid 367 through 386 )

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