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- PDB-3uvi: tRNA-guanine transglycosylase C158S C281S W326E E339Q mutant -

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Basic information

Entry
Database: PDB / ID: 3uvi
TitletRNA-guanine transglycosylase C158S C281S W326E E339Q mutant
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / TGT / DIMER INTERFACE / GLYCOSYLTRANSFERASE / METAL-BINDING / QUEUOSINE BIOSYNTHESIS / TRNA PROCESSING / Zinc Binding / Guanine Binding
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
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
IODIDE ION / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJakobi, S. / Heine, A. / Klebe, G.
CitationJournal: Proteins / Year: 2014
Title: Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme.
Authors: Jakobi, S. / Nguyen, T.X. / Debaene, F. / Metz, A. / Sanglier-Cianferani, S. / Reuter, K. / Klebe, G.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Aug 19, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_biol / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 13, 2023Group: 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

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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)44,57817
Polymers42,9801
Non-polymers1,59816
Water8,629479
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,15534
Polymers85,9592
Non-polymers3,19632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8610 Å2
ΔGint-68 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.019, 64.984, 70.488
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-446-

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: 42979.621 Da / Num. of mol.: 1 / Mutation: C158S, C281S, W326E, E339Q
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

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Non-polymers , 6 types, 495 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 49.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Sodium iodide 0.2M, PEG 3350 20% w/v, pH 7.8, 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: Mar 16, 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: 1.55→50 Å / Num. all: 58805 / Num. obs: 58805 / % possible obs: 99 % / Redundancy: 3 % / Biso Wilson estimate: 10.68 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.08
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.78 / Num. unique all: 2729 / Rsym value: 0.274 / % possible all: 89.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.55→35.076 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: R_FREE / σ(F): 1.36 / Phase error: 17.82 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 2970 5.06 %RANDOM
Rwork0.1647 ---
all0.166 58805 --
obs0.166 58746 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.838 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso mean: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.8851 Å2-0 Å2-1.1094 Å2
2---0.5744 Å2-0 Å2
3----1.3107 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 39 479 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063145
X-RAY DIFFRACTIONf_angle_d1.0544267
X-RAY DIFFRACTIONf_dihedral_angle_d12.741239
X-RAY DIFFRACTIONf_chiral_restr0.07452
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5496-1.5750.2831090.22922416X-RAY DIFFRACTION90
1.575-1.60220.24351390.21442601X-RAY DIFFRACTION97
1.6022-1.63130.22711470.19722628X-RAY DIFFRACTION98
1.6313-1.66270.2141190.19022659X-RAY DIFFRACTION100
1.6627-1.69660.21611510.18042692X-RAY DIFFRACTION100
1.6966-1.73350.20251410.17262649X-RAY DIFFRACTION100
1.7335-1.77380.21131350.17142675X-RAY DIFFRACTION100
1.7738-1.81820.22941370.16412672X-RAY DIFFRACTION100
1.8182-1.86730.16411470.16142709X-RAY DIFFRACTION100
1.8673-1.92230.18691370.16342675X-RAY DIFFRACTION100
1.9223-1.98430.18231660.16022637X-RAY DIFFRACTION100
1.9843-2.05520.18791460.16852681X-RAY DIFFRACTION100
2.0552-2.13750.20641370.1712662X-RAY DIFFRACTION100
2.1375-2.23480.19551600.16062692X-RAY DIFFRACTION100
2.2348-2.35260.16511400.16012654X-RAY DIFFRACTION100
2.3526-2.49990.19341500.15692687X-RAY DIFFRACTION100
2.4999-2.69290.20991390.16092684X-RAY DIFFRACTION100
2.6929-2.96380.16911420.1672695X-RAY DIFFRACTION100
2.9638-3.39230.18881450.15762664X-RAY DIFFRACTION99
3.3923-4.27280.16171380.14212699X-RAY DIFFRACTION99
4.2728-35.08480.19351450.16932645X-RAY DIFFRACTION95

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