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- PDB-7a9e: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -

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Basic information

Entry
Database: PDB / ID: 7a9e
TitletRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with ethyl methyl sulfone
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
1-methylsulfonylethane / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 1, 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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4397
Polymers42,9111
Non-polymers5286
Water4,143230
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,87714
Polymers85,8212
Non-polymers1,05612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2190 Å2
ΔGint-6 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.998, 127.998, 115.379
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-582-

HOH

21A-724-

HOH

31A-729-

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, 236 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-R4W / 1-methylsulfonylethane / trans-3,4-dihydroxysulfolane / ethyl methyl sulfone


Mass: 108.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.24 Å3/Da / Density % sol: 62.08 % / 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, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.76→42.85 Å / Num. obs: 55465 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 28.08 Å2 / CC1/2: 0.999 / Rsym value: 0.089 / Net I/σ(I): 16.9
Reflection shellResolution: 1.76→1.87 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8761 / CC1/2: 0.607 / Rsym value: 1.478 / % possible all: 99.3

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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: 1.76→42.85 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 2774 5 %
Rwork0.1816 52689 -
obs0.1828 55463 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.54 Å2
Refinement stepCycle: LAST / Resolution: 1.76→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 29 230 3118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713037
X-RAY DIFFRACTIONf_angle_d0.79034113
X-RAY DIFFRACTIONf_chiral_restr0.0531439
X-RAY DIFFRACTIONf_plane_restr0.0051552
X-RAY DIFFRACTIONf_dihedral_angle_d15.22411830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.32361350.2792558X-RAY DIFFRACTION99.08
1.79-1.820.2721360.26232587X-RAY DIFFRACTION100
1.82-1.860.27481360.24792583X-RAY DIFFRACTION98.94
1.86-1.90.25451360.22362589X-RAY DIFFRACTION99.74
1.9-1.940.23011370.20622600X-RAY DIFFRACTION99.96
1.94-1.980.24011380.20072612X-RAY DIFFRACTION100
1.98-2.030.24321370.19582613X-RAY DIFFRACTION100
2.03-2.090.22451360.18472578X-RAY DIFFRACTION100
2.09-2.150.23021380.17762615X-RAY DIFFRACTION100
2.15-2.220.20521380.17522624X-RAY DIFFRACTION100
2.22-2.30.20441380.17612627X-RAY DIFFRACTION100
2.3-2.390.21231360.1772584X-RAY DIFFRACTION98.69
2.39-2.50.21671380.17952624X-RAY DIFFRACTION99.5
2.5-2.630.2031390.17292636X-RAY DIFFRACTION100
2.63-2.790.19721390.1742649X-RAY DIFFRACTION100
2.79-3.010.2031390.17752648X-RAY DIFFRACTION99.96
3.01-3.310.15521410.17412675X-RAY DIFFRACTION100
3.31-3.790.18571410.16382671X-RAY DIFFRACTION99.12
3.79-4.770.17741440.15962735X-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)
10.6699668759280.750866395487-0.3039412734891.140445618760.3630183554290.9928173641980.03967959367450.115801124510.14564018166-0.100893112071-0.0824412526071-0.00357796588318-0.12426428577-0.003610353777815.64266563525E-50.2711094557140.0322807130212-0.04259567737720.216113773564-0.004381045621070.2399062243819.0892032208441.5473231133-13.4551228735
20.177043731476-0.06858185307370.1510222121060.4607005690930.2033777177660.2188348777380.1659311098140.0504608728462-0.042010954990.133766214067-0.0100178679657-0.1305532142240.001212617094380.03242919556110.001782955707450.268012838249-0.0350546080972-0.06777280599280.240424588646-0.03160346444050.29157007337725.549340172240.3268728643-5.00857528007
31.02213897323-0.109752173011-0.07499930796281.24557511809-0.1838445679380.5077182415630.207081168291-0.1457101140090.07322277631870.52503418506-0.0300790649181-0.4856427424890.08876957831640.08504493770270.1652123807340.416041695675-0.0816286389883-0.1268556480340.249388977846-0.05949260820790.3304372399324.342633023446.5205633183.63917502868
41.42340627227-0.05532270696581.075188016540.8018555891730.2603183195460.7469728742950.0905069964421-0.4286906147140.3405758364790.229450988529-0.236274767250.0398588274097-0.17133646767-0.393044257541-0.1608393278380.433415060282-0.09121219756680.01230757318220.355090520836-0.1461840110790.32301313419713.831742788553.23173623617.68199142505
52.048252051860.4285420600340.6355836091491.031414262461.000440429560.8941112242120.104354246426-0.5246313483230.3385473898910.147979597453-0.2788546330040.186272461796-0.172642087553-0.210044822262-0.01329995080120.3175144446980.03221290636130.004852563158850.307750474053-0.107142419070.2891289412544.0270951508348.38667408172.86553499869
60.196418403733-0.371285549912-0.01319532888890.4221301401770.6074400593080.5245199683470.0377647931457-0.2580620842190.1098510853870.21898189646-0.002324280860980.0387988059093-0.0237503058399-0.0552843634602-1.02887976354E-50.249201600691-0.00146571490614-0.04909487846580.2747322873960.01378918935380.2267175421197.126764049325.436768375-0.192864316946
72.07049482849-0.4102426197410.8968736495080.742027686274-0.02820612314760.815687737350.3049617362580.00648134068694-0.277359267413-0.193424920112-0.2069640839010.2383777899550.101619213304-0.0433786558150.1174463490920.222843681657-0.00607172695514-0.06921976596390.2124450883180.006852214743010.2176596012346.7783708332620.0152053824-8.16899534823
80.294159756052-0.3079666758680.09320043043271.67752369079-0.06734562358710.2292934310420.104090426956-0.145944084477-0.3425725894520.338207278395-0.08270480291511.30471073258-0.0273920379018-0.501551954715-0.05715148213080.232498788843-0.01085555725080.00469354909270.391658534097-0.06723414693080.434012152847-8.586428788328.4664426348-3.56216606162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 274 )
6X-RAY DIFFRACTION6chain 'A' and (resid 275 through 304 )
7X-RAY DIFFRACTION7chain 'A' and (resid 305 through 366 )
8X-RAY DIFFRACTION8chain 'A' and (resid 367 through 386 )

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