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- PDB-7apl: tRNA-guanine transglycosylase G87C mutant spin-labeled with MTSL -

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Basic information

Entry
Database: PDB / ID: 7apl
TitletRNA-guanine transglycosylase G87C mutant spin-labeled with MTSL
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / enzyme / spin label
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine 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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsNguyen, D. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)324043133 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance.
Authors: Nguyen, D. / Abdullin, D. / Heubach, C.A. / Pfaffeneder, T. / Nguyen, A. / Heine, A. / Reuter, K. / Diederich, F. / Schiemann, O. / Klebe, G.
History
DepositionOct 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5184
Polymers43,2681
Non-polymers2503
Water3,063170
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0358
Polymers86,5362
Non-polymers4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4290 Å2
ΔGint-23 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.542, 90.947, 167.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 43268.070 Da / Num. of mol.: 1 / Mutation: G87R1/C158S/C281S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.78 % / Description: rhombohedral
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 7% PEG 8000, 10% DMSO

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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: 1.99→44.59 Å / Num. obs: 35628 / % possible obs: 97.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 33.84 Å2 / CC1/2: 0.998 / Rsym value: 0.063 / Net I/σ(I): 15.2
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5311 / CC1/2: 0.887 / Rsym value: 0.498 / % possible all: 97.6

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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: 1P0D

1p0d


Resolution: 1.99→44.59 Å / SU ML: 0.1919 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1682 5 %
Rwork0.1717 31942 -
obs0.1736 33624 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.69 Å2
Refinement stepCycle: LAST / Resolution: 1.99→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 13 170 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642993
X-RAY DIFFRACTIONf_angle_d0.79644053
X-RAY DIFFRACTIONf_chiral_restr0.048430
X-RAY DIFFRACTIONf_plane_restr0.0051544
X-RAY DIFFRACTIONf_dihedral_angle_d17.62341802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.26561360.20422586X-RAY DIFFRACTION97.14
2.05-2.110.24491380.19222616X-RAY DIFFRACTION97.97
2.11-2.190.26111410.19182672X-RAY DIFFRACTION98.67
2.19-2.280.21271390.18132643X-RAY DIFFRACTION98.37
2.28-2.380.23791390.16962650X-RAY DIFFRACTION99.04
2.38-2.510.24351410.17182666X-RAY DIFFRACTION98.77
2.51-2.660.20761410.18222680X-RAY DIFFRACTION98.57
2.66-2.870.23661320.17762525X-RAY DIFFRACTION93.82
2.87-3.160.1941440.17422721X-RAY DIFFRACTION99.31
3.16-3.610.20451420.1712701X-RAY DIFFRACTION99.2
3.61-4.550.17621440.15292746X-RAY DIFFRACTION99.18
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)
10.1624478775810.0490057880602-0.1097614209050.205671309461-0.1342143330430.2393762953750.140153600778-0.195536026014-0.02254234244080.121648923862-0.0886646945353-6.34935037247E-50.01637411760570.02564677956046.97363038282E-50.256697241447-0.07134970077880.03191731893080.279816181064-0.01316458091540.25855435499423.194965352313.485447469616.9989640838
20.168320423965-0.1293858018170.06856670038530.2645305477310.02732435552030.4004234107590.30402118967-0.374164777770.08435043271780.419614652196-0.2990285214680.223421589460.19088693214-0.1627082087230.1458053510730.422742155846-0.1662104523760.1453209380850.463797504468-0.05121176078260.377783976186.970832910342.5726871108424.0898341813
30.0586195632920.1634554401680.1104418444410.5006125156810.4082741028640.3492587291150.271741384307-0.2564489737580.1764721380490.536781361262-0.1668750375170.2229473401580.145352473894-0.4453593335040.1616126994310.518406085763-0.09906559209320.2779099512250.674210056197-0.060074391680.3693855493996.0344160788315.874537968132.0839204712
40.447902864480.293902368139-0.3188543370830.352254144955-0.1166410678660.3112427622240.200214227876-0.3047831099040.3452727139220.3555955542940.015379516650.32116131916-0.180027269479-0.2979674150590.001977212583350.435573128601-0.05911519647140.1493859275440.424759657113-0.08150881341770.40132336306112.793464355723.546967126824.8789469858
50.0438253267418-0.0405147653185-0.03357468433810.0571691588670.06009471079510.05952359080430.0970131991105-0.0224181382530.221937898624-0.0618441689733-0.116455743930.278424284863-0.334029818396-0.116761801099-6.97404875069E-50.2913326006870.02528788499370.01231069826540.287100754883-0.01874702840530.36664317382310.76500727317.15561723423.27150116658
60.221226276227-0.0919437287712-0.1714486961910.2175644744060.07126653028020.1365059840320.0673983783360.07473373785710.170518230885-0.167916527644-0.0765107455780.0528353892143-0.1913179679960.03261265810361.27196875175E-50.300852896140.01848995879230.02279747439550.255351456730.03559680729820.32584429604317.362463127914.08141263-3.82077468061
70.006415013908630.003577938975760.01892859553710.006277682512680.01036686282460.04236017524910.0377529401474-0.03729675470690.368267250709-0.2354402792710.023745074035-0.0120333047863-0.313735948781-0.0316928659543-0.0002298817034590.447553513646-0.00321224276830.03909691485370.2513020091120.02679599821420.45403213256419.883192650631.72839038683.75415952333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 70 )A10 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 147 )A71 - 147
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 188 )A148 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 274 )A189 - 274
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 304 )A275 - 304
6X-RAY DIFFRACTION6chain 'A' and (resid 305 through 366 )A305 - 366
7X-RAY DIFFRACTION7chain 'A' and (resid 367 through 384 )A367 - 384

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