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- PDB-7adn: apo tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant -

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Basic information

Entry
Database: PDB / ID: 7adn
Titleapo tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / enzyme / disulfide
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
FORMIC ACID / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsNguyen, D. / You, S. / 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
DepositionSep 15, 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 20, 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)43,2065
Polymers42,9111
Non-polymers2964
Water3,657203
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,41210
Polymers85,8212
Non-polymers5918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2210 Å2
ΔGint-12 kcal/mol
Surface area29240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.864, 127.864, 115.486
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-695-

HOH

21A-702-

HOH

31A-703-

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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 61.27 % / Description: hexagonal bipyramidal
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→42.85 Å / Num. obs: 43128 / % possible obs: 99.7 % / Redundancy: 24.8 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 0.999 / Rsym value: 0.062 / Net I/σ(I): 31.6
Reflection shellResolution: 1.92→2.03 Å / Redundancy: 20 % / Num. unique obs: 6777 / CC1/2: 0.963 / Rsym value: 0.493 / % possible all: 98.5

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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: 1.92→42.85 Å / SU ML: 0.1576 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.7893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 2156 5 %
Rwork0.1716 40956 -
obs0.1724 43112 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.15 Å2
Refinement stepCycle: LAST / Resolution: 1.92→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 0 16 203 3063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673053
X-RAY DIFFRACTIONf_angle_d0.79454134
X-RAY DIFFRACTIONf_chiral_restr0.0519436
X-RAY DIFFRACTIONf_plane_restr0.0058557
X-RAY DIFFRACTIONf_dihedral_angle_d13.67761848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.960.25141360.21712587X-RAY DIFFRACTION96.32
1.96-2.010.21741410.19782676X-RAY DIFFRACTION99.89
2.01-2.060.24061420.20112710X-RAY DIFFRACTION99.89
2.06-2.120.20281410.18742671X-RAY DIFFRACTION99.93
2.12-2.190.21851420.1752699X-RAY DIFFRACTION99.96
2.19-2.270.18421420.17222699X-RAY DIFFRACTION100
2.27-2.360.16081430.16512718X-RAY DIFFRACTION100
2.36-2.470.22761420.17742699X-RAY DIFFRACTION99.96
2.47-2.60.20441430.18352720X-RAY DIFFRACTION99.93
2.6-2.760.19611430.18312716X-RAY DIFFRACTION100
2.76-2.980.24731450.18552745X-RAY DIFFRACTION99.9
2.98-3.280.19241450.17622748X-RAY DIFFRACTION99.97
3.28-3.750.16741460.16632780X-RAY DIFFRACTION100
3.75-4.720.15221480.1412808X-RAY DIFFRACTION100
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)
10.3696560304880.38588504731-0.07701040634080.9819478443380.6181754879640.8061070769080.02323020593910.05459625473090.078915797127-0.0925739834582-0.0871193971661-0.00205733016524-0.1323118672950.00998811777154-8.60310127106E-50.2862625749160.0161485753095-0.02885036293790.236053906912-0.01158840463250.2665350622878.4727686078841.0954210555-12.3486227129
21.337498414460.5219745063070.2045292996491.005209299350.2990545861090.3968246518930.180534297572-0.0162540747565-0.02451194208830.287133815812-0.124866336624-0.310195969168-0.05301039891040.186272982227-0.01420992718420.378088494642-0.0979636157326-0.0955373651520.242669974543-0.02035787037570.31459840738924.234677210944.1620381870.620461311162
30.889643507644-0.448848245656-0.004664855847880.3277649277690.2175279923630.4703067174190.11648652158-0.2963376696950.3409127517890.208024318815-0.189172454101-0.0241246243182-0.217602028292-0.208299237282-0.1960494763140.533328483305-0.1400858412590.01207177109620.327358086181-0.1361976624620.31803815251913.658253620353.53822151197.21402352319
41.535906234570.3178236849840.3695174702640.6300663841440.7414615587871.087831223920.158807400141-0.4200275315180.3245558180280.14183690672-0.2469903877310.175643069332-0.29472801642-0.220337402486-0.0005289154703920.3627631155490.0006137310741980.01175369150030.307420098049-0.1146189656470.3127731284563.3169447801448.251242073.03975187567
51.69318823167-1.008944336740.3578566424830.810499970493-0.2645603585710.5726956071010.10712229487-0.138578737094-0.11295292745-0.023824031755-0.08782897870070.09525775289250.0463818631791-0.0560725269344-3.70293951378E-50.241560181166-0.0288490682292-0.06111509388650.2410061077910.0175391363650.2265944793686.828317260721.5899051099-5.82877519382
60.1803022031970.06655131688930.07569178086210.691570132958-0.02350863000310.1077650590230.274003648817-0.167774437292-0.2324130935040.178582697807-0.1769790565611.16566341769-0.0469780531407-0.163679954542-0.004496043306240.260354760387-0.02509284643850.02481258795580.410936793055-0.06174423204370.427814946027-8.680550814528.2331489173-3.60512836228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 188 )
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 274 )
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 366 )
6X-RAY DIFFRACTION6chain 'A' and (resid 367 through 386 )

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