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- PDB-4htb: tRNA-guanine transglycosylase Y330C mutant in space group C2 -

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Basic information

Entry
Database: PDB / ID: 4htb
TitletRNA-guanine transglycosylase Y330C mutant in space group C2
ComponentstRNA-guanine transglycosylase
KeywordsTRANSFERASE / Protein-Protein-Interface / Dimer Interface / TGT / tRNA / guanine
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: 1.9 Å
AuthorsJakobi, S. / 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
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 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 1.3Aug 19, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...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_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_assembly_prop.biol_id / _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 1.4Sep 20, 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

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Assembly

Deposited unit
A: tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5087
Polymers43,0101
Non-polymers4986
Water4,900272
1
A: tRNA-guanine transglycosylase
hetero molecules

A: tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01614
Polymers86,0202
Non-polymers99612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4980 Å2
ΔGint-16 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.968, 64.660, 70.563
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

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Components

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


Mass: 43009.797 Da / Num. of mol.: 1 / Mutation: Y330C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ATCC 31821 / ZM4 / CP4 / 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.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 48.78 %
Crystal growTemperature: 293 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 293K

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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 15, 2012 / 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: 1.9→30 Å / Num. obs: 31561 / % possible obs: 98.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 20.72 Å2 / Rsym value: 0.102 / Net I/σ(I): 9.49
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1565 / Rsym value: 0.342 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUD

1pud


Resolution: 1.9→29.141 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1599 5.07 %Random
Rwork0.1799 ---
obs0.1816 31527 97.76 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.192 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.496 Å2-0 Å2-0.8169 Å2
2---8.425 Å20 Å2
3---0.929 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 27 272 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052942
X-RAY DIFFRACTIONf_angle_d0.9063966
X-RAY DIFFRACTIONf_dihedral_angle_d12.4441089
X-RAY DIFFRACTIONf_chiral_restr0.062422
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8996-1.96090.30721240.24882676X-RAY DIFFRACTION96
1.9609-2.0310.2711510.22972734X-RAY DIFFRACTION100
2.031-2.11230.26171520.21062728X-RAY DIFFRACTION99
2.1123-2.20840.2421640.20412738X-RAY DIFFRACTION99
2.2084-2.32480.25751460.18872775X-RAY DIFFRACTION99
2.3248-2.47040.22451410.18242720X-RAY DIFFRACTION99
2.4704-2.6610.21341360.17642765X-RAY DIFFRACTION99
2.661-2.92850.19751470.17372733X-RAY DIFFRACTION98
2.9285-3.35180.22391370.16342726X-RAY DIFFRACTION98
3.3518-4.22080.17221490.14812691X-RAY DIFFRACTION96
4.2208-29.14430.1921520.18362642X-RAY DIFFRACTION93

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