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- PDB-5xob: Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase) -

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Basic information

Entry
Database: PDB / ID: 5xob
TitleCrystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)
ComponentstRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
KeywordsLIGASE / zinc ribbon / conformational change / TiaS / tRNA modification / Zinc finger engineering
Function / homology
Function and homology information


tRNAIle2-agmatinylcytidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA wobble cytosine modification / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF1743 / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / Domain of unknown function (DUF1743) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.48 Å
AuthorsDong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
Authors: Dong, J. / Li, F. / Gao, F. / Wei, J. / Lin, Y. / Zhang, Y. / Lou, J. / Liu, G. / Dong, Y. / Liu, L. / Liu, H. / Wang, J. / Gong, W.
History
DepositionMay 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4623
Polymers48,3721
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.926, 68.926, 211.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / tRNA(Ile2)-agm2C synthetase / tRNA(Ile2) agmatidine synthetase


Mass: 48372.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: tiaS, AF_2259 / Production host: Escherichia coli (E. coli)
References: UniProt: O28025, tRNAIle2-agmatinylcytidine synthase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 50mM HEPES-Na pH7.0-7.2, 0.5M NH4Ac, 0.2M MgCl2, 1.5-2.5% PEG 8000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 18539 / % possible obs: 99.1 % / Redundancy: 11.6 % / Net I/σ(I): 21.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.48→49.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.395 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29439 962 5.22 %RANDOM
Rwork0.24465 ---
obs0.24518 18414 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.054 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å20 Å20 Å2
2--3.85 Å2-0 Å2
3----7.7 Å2
Refinement stepCycle: 1 / Resolution: 2.48→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 2 0 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193348
X-RAY DIFFRACTIONr_bond_other_d0.0010.023226
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9724533
X-RAY DIFFRACTIONr_angle_other_deg0.74137424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55423.782156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.921526
X-RAY DIFFRACTIONr_chiral_restr0.0670.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.098.0751666
X-RAY DIFFRACTIONr_mcbond_other3.0898.0741665
X-RAY DIFFRACTIONr_mcangle_it5.23712.12079
X-RAY DIFFRACTIONr_mcangle_other5.23612.1022080
X-RAY DIFFRACTIONr_scbond_it3.2588.5721682
X-RAY DIFFRACTIONr_scbond_other3.2588.5721682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.71412.6492454
X-RAY DIFFRACTIONr_long_range_B_refined8.47962.9233590
X-RAY DIFFRACTIONr_long_range_B_other8.47862.9343591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.477→2.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 12 -
Rwork0.359 1310 -
obs--97.06 %

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