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- PDB-4dy1: tRNA-guanine transglycosylase F92C C158S C281S mutant -

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Basic information

Entry
Database: PDB / ID: 4dy1
TitletRNA-guanine transglycosylase F92C C158S C281S mutant
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / functional dimer / protein-protein interface / guanine exchange enzyme / zinc binding / guanine binding / tRNA binding
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
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.045 Å
AuthorsJakobi, S. / Heine, A. / Klebe, G.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt.
Authors: Jakobi, S. / Nguyen, P.T. / Debaene, F. / Cianferani, S. / Reuter, K. / Klebe, G.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,1604
Polymers42,9941
Non-polymers1663
Water6,521362
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3208
Polymers85,9872
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3870 Å2
ΔGint-119 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.828, 64.601, 71.092
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

DetailsMONOMER IN SOLUTION, MONOMERIC FORM PROVEN WITH NATIVE MASS SPECTROMETRY (NANO-ESI MS), DIMERIC IN CRYSTAL PACKING

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Components

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


Mass: 42993.672 Da / Num. of mol.: 1 / Mutation: F92C, C158S, C281S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt, ZMO0363 / Plasmid: pASK-IBA13Plus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIPL
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID AT POSITION 312 IS LYS. PLEASE SEE REUTER K.K.H. ET AL [J. BACTERIOL. 177:5284-5288(1995)].

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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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS 0.1M, DMSO 10%, PEG8000 7%, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2011 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.045→50 Å / Num. all: 25405 / Num. obs: 25405 / % possible obs: 97.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.1 / Net I/σ(I): 11.6
Reflection shellResolution: 2.045→2.09 Å / Redundancy: 2.3 % / Num. unique all: 1085 / Rsym value: 0.375 / % possible all: 84.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 2.045→25.158 Å / SU ML: 0.24 / Isotropic thermal model: isotropic / Cross valid method: R_FREE / σ(F): 0 / Phase error: 21.75 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1203 5.08 %RANDOM
Rwork0.1655 ---
obs0.1683 23698 91.16 %-
all-23698 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.878 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.6715 Å2-0 Å2-0.861 Å2
2---2.4108 Å20 Å2
3----1.2607 Å2
Refinement stepCycle: LAST / Resolution: 2.045→25.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 3 362 3223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072986
X-RAY DIFFRACTIONf_angle_d1.0534034
X-RAY DIFFRACTIONf_dihedral_angle_d13.6911132
X-RAY DIFFRACTIONf_chiral_restr0.066425
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.045-2.12640.2711160.20092002X-RAY DIFFRACTION74
2.1264-2.22310.2971220.2022327X-RAY DIFFRACTION84
2.2231-2.34020.30991140.2432173X-RAY DIFFRACTION80
2.3402-2.48670.25951390.17382503X-RAY DIFFRACTION93
2.4867-2.67850.23191210.17332656X-RAY DIFFRACTION95
2.6785-2.94770.24751420.1572643X-RAY DIFFRACTION97
2.9477-3.37340.19791330.15382696X-RAY DIFFRACTION98
3.3734-4.24680.17961490.13392718X-RAY DIFFRACTION99
4.2468-25.15970.18361670.15712777X-RAY DIFFRACTION99

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