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- PDB-4dxx: TGT K52M mutant crystallized at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 4dxx
TitleTGT K52M mutant crystallized at pH 8.5
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / functional dimer / dimer interface / guanine exchange enzyme / zinc binding / guanine binding / tRNA 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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsJakobi, S. / Ritschel, T. / 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
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: 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 1.4Sep 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)43,3206
Polymers42,9281
Non-polymers3925
Water7,584421
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,63912
Polymers85,8552
Non-polymers78410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5160 Å2
ΔGint-4 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.220, 64.865, 70.082
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

21A-842-

HOH

Detailslow amount of monomer in solution, monomeric form proven with native mass spectrometry

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Components

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


Mass: 42927.723 Da / Num. of mol.: 1 / Mutation: K52M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt, ZMO0363 / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS 0.1M, DMSO 10%, PEG8000 12%, 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: Dec 9, 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: 1.66→50 Å / Num. all: 47912 / Num. obs: 47912 / % possible obs: 99.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.049 / Net I/σ(I): 18.1
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2330 / Rsym value: 0.285 / % possible all: 96.6

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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: 1.66→34.85 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / Cross valid method: R_FREE / σ(F): 1.35 / Phase error: 18.21 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2417 5.05 %RANDOM
Rwork0.1658 ---
obs0.1675 47886 99.56 %-
all-47886 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.963 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso mean: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2368 Å2-0 Å2-0.6721 Å2
2---1.2512 Å20 Å2
3---1.0144 Å2
Refinement stepCycle: LAST / Resolution: 1.66→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 19 421 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063083
X-RAY DIFFRACTIONf_angle_d1.0844177
X-RAY DIFFRACTIONf_dihedral_angle_d12.9361159
X-RAY DIFFRACTIONf_chiral_restr0.07447
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.69430.25211250.22492643X-RAY DIFFRACTION98
1.6943-1.73110.21741300.19952652X-RAY DIFFRACTION100
1.7311-1.77140.19361490.17832644X-RAY DIFFRACTION100
1.7714-1.81570.18891540.16332661X-RAY DIFFRACTION100
1.8157-1.86480.19611440.15382705X-RAY DIFFRACTION100
1.8648-1.91970.20771210.16592645X-RAY DIFFRACTION100
1.9197-1.98160.18381340.16492698X-RAY DIFFRACTION100
1.9816-2.05240.20361280.15982659X-RAY DIFFRACTION100
2.0524-2.13460.20321470.16132678X-RAY DIFFRACTION100
2.1346-2.23170.21351390.16372697X-RAY DIFFRACTION100
2.2317-2.34940.21111290.16572674X-RAY DIFFRACTION100
2.3494-2.49650.19511650.1592668X-RAY DIFFRACTION100
2.4965-2.68920.20171380.1632707X-RAY DIFFRACTION100
2.6892-2.95970.18611550.16392677X-RAY DIFFRACTION100
2.9597-3.38770.18741460.16342668X-RAY DIFFRACTION100
3.3877-4.26690.18491520.15192712X-RAY DIFFRACTION100
4.2669-34.85720.21441610.17822681X-RAY DIFFRACTION97

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