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- PDB-7apm: tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL. -

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Basic information

Entry
Database: PDB / ID: 7apm
TitletRNA-guanine transglycosylase H319C 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 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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
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
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct.title
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

Downloads & links

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5646
Polymers43,1871
Non-polymers3775
Water5,675315
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,12812
Polymers86,3742
Non-polymers75410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4850 Å2
ΔGint-42 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.911, 65.064, 70.813
Angle α, β, γ (deg.)90.000, 96.288, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

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Components

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


Mass: 43186.980 Da / Num. of mol.: 1 / Mutation: C158S/C281S/H319R1
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES, pH 5.5, 0.5 mM DTT, 13% 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: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.66→45.68 Å / Num. obs: 47688 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 0.997 / Rsym value: 0.075 / Net I/σ(I): 10.4
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7302 / CC1/2: 0.82 / Rsym value: 0.466 / % possible all: 92.8

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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: 1.66→45.68 Å / SU ML: 0.1905 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.0193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1758 2385 5 %
Rwork0.1393 45298 -
obs0.1412 47683 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.66→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 20 315 3196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793048
X-RAY DIFFRACTIONf_angle_d0.93444128
X-RAY DIFFRACTIONf_chiral_restr0.0517432
X-RAY DIFFRACTIONf_plane_restr0.0065553
X-RAY DIFFRACTIONf_dihedral_angle_d16.50531836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.2831170.28212221X-RAY DIFFRACTION82.64
1.7-1.730.33341400.23242657X-RAY DIFFRACTION98.28
1.73-1.770.26991440.17932729X-RAY DIFFRACTION99
1.77-1.820.20771420.14792701X-RAY DIFFRACTION99.23
1.82-1.870.17041400.12972662X-RAY DIFFRACTION98.91
1.87-1.920.19051420.12492706X-RAY DIFFRACTION98.89
1.92-1.980.18251400.13152660X-RAY DIFFRACTION98.94
1.98-2.060.17871420.13372695X-RAY DIFFRACTION98.51
2.06-2.140.16471420.12642685X-RAY DIFFRACTION98.67
2.14-2.230.17211400.11952679X-RAY DIFFRACTION98.05
2.23-2.350.16921410.12042662X-RAY DIFFRACTION96.99
2.35-2.50.15971380.12282636X-RAY DIFFRACTION97.16
2.5-2.690.16791430.12982709X-RAY DIFFRACTION98.65
2.69-2.960.16871430.13292717X-RAY DIFFRACTION98.86
2.96-3.390.16621410.13952681X-RAY DIFFRACTION98.5
3.39-4.270.17151430.13092718X-RAY DIFFRACTION98.76

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