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- PDB-3unt: tRNA-guanine transglycosylase E339Q mutant -

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Basic information

Entry
Database: PDB / ID: 3unt
TitletRNA-guanine transglycosylase 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-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: 1.801 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 16, 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 1.3Sep 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_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)43,4896
Polymers43,0691
Non-polymers4205
Water7,188399
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,97712
Polymers86,1382
Non-polymers84010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4790 Å2
ΔGint-12 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.290, 64.890, 70.238
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

21A-734-

HOH

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Components

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


Mass: 43068.844 Da / Num. of mol.: 1 / Mutation: 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
#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-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS 0.1M, DMSO 10% v/v, PEG8000 7% w/w, 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: Oct 13, 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: 1.8→30 Å / Num. all: 36234 / Num. obs: 36234 / % possible obs: 95.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.089 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1618 / Rsym value: 0.283 / % possible all: 87.5

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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: 1.801→18.917 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: R_FREE / σ(F): 1.36 / Phase error: 17.91 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 1796 4.96 %RANDOM
Rwork0.1536 ---
all0.1552 36210 --
obs0.1552 36210 95.67 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.078 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.7797 Å2-0 Å2-0.415 Å2
2---1.9215 Å20 Å2
3----0.8582 Å2
Refinement stepCycle: LAST / Resolution: 1.801→18.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 23 399 3260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072994
X-RAY DIFFRACTIONf_angle_d1.0364055
X-RAY DIFFRACTIONf_dihedral_angle_d12.5271111
X-RAY DIFFRACTIONf_chiral_restr0.068434
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84910.24561180.20342421X-RAY DIFFRACTION88
1.8491-1.90350.27921120.18922563X-RAY DIFFRACTION92
1.9035-1.96490.21011410.16612595X-RAY DIFFRACTION95
1.9649-2.0350.20721280.15532693X-RAY DIFFRACTION97
2.035-2.11640.1981370.15662671X-RAY DIFFRACTION97
2.1164-2.21260.19451460.14922691X-RAY DIFFRACTION98
2.2126-2.32910.19491370.14712737X-RAY DIFFRACTION98
2.3291-2.47470.19881380.1472681X-RAY DIFFRACTION98
2.4747-2.66530.17921420.15262714X-RAY DIFFRACTION98
2.6653-2.93260.19321640.15042691X-RAY DIFFRACTION98
2.9326-3.35490.14331350.14532683X-RAY DIFFRACTION97
3.3549-4.21910.15031490.13582652X-RAY DIFFRACTION95
4.2191-18.91790.18521490.16412613X-RAY DIFFRACTION92

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